Methods for identifying a target site of a cas9 nuclease

ABSTRACT

Some aspects of this disclosure provide strategies, methods, and reagents for determining nuclease target site preferences and specificity of site-specific endonucleases. Some methods provided herein utilize a novel “one-cut” strategy for screening a library of concatemers comprising repeat units of candidate nuclease target sites and constant insert regions to identify library members that can been cut by a nuclease of interest via sequencing of an intact target site adjacent and identical to a cut target site.

RELATED APPLICATION

This application claims priority under 35 U.S.C. §119(e) to U.S.provisional patent application, U.S. Ser. No. 61/864,289, filed Aug. 9,2013, the entire contents of which are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with U.S. Government support under grant numbersHR0011-11-2-0003 and N66001-12-C-4207, awarded by the Defense AdvancedResearch Projects Agency. The U.S. Government has certain rights in theinvention.

BACKGROUND OF THE INVENTION

Site-specific endonucleases theoretically allow for the targetedmanipulation of a single site within a genome and are useful in thecontext of gene targeting as well as for therapeutic applications. In avariety of organisms, including mammals, site-specific endonucleaseshave been used for genome engineering by stimulating eithernon-homologous end joining or homologous recombination. In addition toproviding powerful research tools, site-specific nucleases also havepotential as gene therapy agents, and two site-specific endonucleaseshave recently entered clinical trials: one, CCR5-2246, targeting a humanCCR-5 allele as part of an anti-HIV therapeutic approach (NCT00842634,NCT01044654, NCT01252641), and the other one, VF24684, targeting thehuman VEGF-A promoter as part of an anti-cancer therapeutic approach(NCT01082926).

Specific cleavage of the intended nuclease target site without or withonly minimal off-target activity is a prerequisite for clinicalapplications of site-specific endonuclease, and also for high-efficiencygenomic manipulations in basic research applications, as imperfectspecificity of engineered site-specific binding domains has been linkedto cellular toxicity and undesired alterations of genomic loci otherthan the intended target. Most nucleases available today, however,exhibit significant off-target activity, and thus may not be suitablefor clinical applications. Technology for evaluating nucleasespecificity and for engineering nucleases with improved specificity aretherefore needed.

SUMMARY OF THE INVENTION

Some aspects of this disclosure are based on the recognition that thereported toxicity of some engineered site-specific endonucleases isbased on off-target DNA cleavage, rather than on off-target bindingalone. Some aspects of this disclosure provide strategies, compositions,systems, and methods to evaluate and characterize the sequencespecificity of site-specific nucleases, for example, RNA-programmableendonucleases, such as Cas9 endonucleases, zinc finger nucleases (ZNFs),homing endonucleases, or transcriptional activator-like elementnucleases (TALENs).

The strategies, methods, and reagents of the present disclosurerepresent, in some aspects, an improvement over previous methods forassaying nuclease specificity. For example, some previously reportedmethods for determining nuclease target site specificity profiles byscreening libraries of nucleic acid molecules comprising candidatetarget sites relied on a “two-cut” in vitro selection method whichrequires indirect reconstruction of target sites from sequences of twohalf-sites resulting from two adjacent cuts of the nuclease of a librarymember nucleic acid (see e.g., PCT Application WO 2013/066438; andPattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R. Revealingoff-target cleavage specificities of zinc-finger nucleases by in vitroselection. Nature methods 8, 765-770 (2011), the entire contents of eachof which are incorporated herein by reference). In contrast to such“two-cut” strategies, the methods of the present disclosure utilize anoptimized “one cut” screening strategy, which allows for theidentification of library members that have been cut at least once bythe nuclease. As explained in more detail elsewhere herein, the“one-cut” selection strategies provided herein are compatible withsingle end high-throughput sequencing methods and do not requirecomputational reconstruction of cleaved target sites from cuthalf-sites, thus streamlining the nuclease profiling process.

Some aspects of this disclosure provide in vitro selection methods forevaluating the cleavage specificity of endonucleases and for selectingnucleases with a desired level of specificity. Such methods are useful,for example, for characterizing an endonuclease of interest and foridentifying a nuclease exhibiting a desired level of specificity, forexample, for identifying a highly specific endonuclease for clinicalapplications.

Some aspects of this disclosure provide methods of identifying suitablenuclease target sites that are sufficiently different from any othersite within a genome to achieve specific cleavage by a given nucleasewithout any or at least minimal off-target cleavage. Such methods areuseful for identifying candidate nuclease target sites that can becleaved with high specificity on a genomic background, for example, whenchoosing a target site for genomic manipulation in vitro or in vivo.

Some aspects of this disclosure provide methods of evaluating,selecting, and/or designing site-specific nucleases with enhancedspecificity as compared to current nucleases. For example, providedherein are methods that are useful for selecting and/or designingsite-specific nucleases with minimal off-target cleavage activity, forexample, by designing variant nucleases with binding domains havingdecreased binding affinity, by lowering the final concentration of thenuclease, by choosing target sites that differ by at least three basepairs from their closest sequence relatives in the genome, and, in thecase of RNA-programmable nucleases, by selecting a guide RNA thatresults in the fewest off-target sites being bound and/or cut.

Compositions and kits useful in the practice of the methods describedherein are also provided.

Some aspects of this disclosure provide methods for identifying a targetsite of a nuclease. In some embodiments, the method comprises (a)providing a nuclease that cuts a double-stranded nucleic acid targetsite, wherein cutting of the target site results in cut nucleic acidstrands comprising a 5′ phosphate moiety; (b) contacting the nuclease of(a) with a library of candidate nucleic acid molecules, wherein eachnucleic acid molecule comprises a concatemer of a sequence comprising acandidate nuclease target site and a constant insert sequence, underconditions suitable for the nuclease to cut a candidate nucleic acidmolecule comprising a target site of the nuclease; and (c) identifyingnuclease target sites cut by the nuclease in (b) by determining thesequence of an uncut nuclease target site on the nucleic acid strandthat was cut by the nuclease in step (b). In some embodiments, thenuclease creates blunt ends. In some embodiments, the nuclease creates a5′ overhang. In some embodiments, the determining of step (c) comprisesligating a first nucleic acid adapter to the 5′ end of a nucleic acidstrand that was cut by the nuclease in step (b) via5′-phosphate-dependent ligation. In some embodiments, the nucleic acidadapter is provided in double-stranded form. In some embodiments, the5′-phosphate-dependent ligation is a blunt end ligation. In someembodiments, the method comprises filling in the 5′-overhang beforeligating the first nucleic acid adapter to the nucleic acid strand thatwas cut by the nuclease. In some embodiments, the determining of step(c) further comprises amplifying a fragment of the concatemer cut by thenuclease that comprises an uncut target site via a PCR reaction using aPCR primer that hybridizes with the adapter and a PCR primer thathybridizes with the constant insert sequence. In some embodiments, themethod further comprises enriching the amplified nucleic acid moleculesfor molecules comprising a single uncut target sequence. In someembodiments, the step of enriching comprises a size fractionation. Insome embodiments, the determining of step (c) comprises sequencing thenucleic acid strand that was cut by the nuclease in step (b), or a copythereof obtained via PCR. In some embodiments, the library of candidatenucleic acid molecules comprises at least 10⁸, at least 10⁹, at least10¹⁰, at least 10¹¹, or at least 10¹² different candidate nucleasecleavage sites. In some embodiments, the nuclease is a therapeuticnuclease which cuts a specific nuclease target site in a gene associatedwith a disease. In some embodiments, the method further comprisesdetermining a maximum concentration of the therapeutic nuclease at whichthe therapeutic nuclease cuts the specific nuclease target site, anddoes not cut more than 10, more than 5, more than 4, more than 3, morethan 2, more than 1, or no additional nuclease target sites. In someembodiments, the method further comprises administering the therapeuticnuclease to a subject in an amount effective to generate a finalconcentration equal or lower than the maximum concentration. In someembodiments, the nuclease is an RNA-programmable nuclease that forms acomplex with an RNA molecule, and wherein the nuclease:RNA complexspecifically binds a nucleic acid sequence complementary to the sequenceof the RNA molecule. In some embodiments, the RNA molecule is asingle-guide RNA (sgRNA). In some embodiments, the sgRNA comprises 5-50nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides,19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. In some embodiments,the nuclease is a Cas9 nuclease. In some embodiments, the nucleasetarget site comprises a [sgRNA-complementary sequence]-[protospaceradjacent motif (PAM)] structure, and the nuclease cuts the target sitewithin the sgRNA-complementary sequence. In some embodiments, thesgRNA-complementary sequence comprises 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. Insome embodiments, the nuclease comprises an unspecific nucleic acidcleavage domain. In some embodiments, the nuclease comprises a FokIcleavage domain. In some embodiments, the nuclease comprises a nucleicacid cleavage domain that cleaves a target sequence upon cleavage domaindimerization. In some embodiments, the nuclease comprises a bindingdomain that specifically binds a nucleic acid sequence. In someembodiments, the binding domain comprises a zinc finger. In someembodiments, the binding domain comprises at least 2, at least 3, atleast 4, or at least 5 zinc fingers. In some embodiments, the nucleaseis a Zinc Finger Nuclease. In some embodiments, the binding domaincomprises a Transcriptional Activator-Like Element. In some embodiments,the nuclease is a Transcriptional Activator-Like Element Nuclease(TALEN). In some embodiments, the nuclease is an organic compound. Insome embodiments, the nuclease comprises an enediyne functional group.In some embodiments, the nuclease is an antibiotic. In some embodiments,the compound is dynemicin, neocarzinostatin, calicheamicin, esperamicin,bleomycin, or a derivative thereof. In some embodiments, the nuclease isa homing endonuclease.

Some aspects of this disclosure provide libraries of nucleic acidmolecules, in which each nucleic acid molecule comprises a concatemer ofa sequence comprising a candidate nuclease target site and a constantinsert sequence of 10-100 nucleotides. In some embodiments, the constantinsert sequence is at least 15, at least 20, at least 25, at least 30,at least 35, at least 40, at least 45, at least 50, at least 55, atleast 60, at least 65, at least 70, at least 75, at least 80, or atleast 95 nucleotides long. In some embodiments, the constant insertsequence is not more than 15, not more than 20, not more than 25, notmore than 30, not more than 35, not more than 40, not more than 45, notmore than 50, not more than 55, not more than 60, not more than 65, notmore than 70, not more than 75, not more than 80, or not more than 95nucleotides long. In some embodiments, the candidate nuclease targetsites are sites that can be cleaved by an RNA-programmable nuclease, aZinc Finger Nuclease (ZFN), a Transcription Activator-Like EffectorNuclease (TALEN), a homing endonuclease, an organic compound nuclease,or an enediyne antibiotic (e.g., dynemicin, neocarzinostatin,calicheamicin, esperamicin, bleomycin). In some embodiments, thecandidate nuclease target site can be cleaved by a Cas9 nuclease. Insome embodiments, the library comprises at least 10⁵, at least 10⁶, atleast 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, orat least 10¹² different candidate nuclease target sites. In someembodiments, the library comprises nucleic acid molecules of a molecularweight of at least 0.5 kDa, at least 1 kDa, at least 2 kDa, at least 3kDa, at least 4 kDa, at least 5 kDa, at least 6 kDa, at least 7 kDa, atleast 8 kDa, at least 9 kDa, at least 10 kDa, at least 12 kDa, or atleast 15 kDa. In some embodiments, the library comprises candidatenuclease target sites that are variations of a known target site of anuclease of interest. In some embodiments, the variations of a knownnuclease target site comprise 10 or fewer, 9 or fewer, 8 or fewer, 7 orfewer, 6 or fewer, 5 or fewer, 4 or fewer, 3 or fewer, or 2 or fewermutations as compared to a known nuclease target site. In someembodiments, the variations differ from the known target site of thenuclease of interest by more than 5%, more than 10%, more than 15%, morethan 20%, more than 25%, or more than 30% on average, distributedbinomially. In some embodiments, the variations differ from the knowntarget site by no more than 10%, no more than 15%, no more than 20%, nomore than 25%, nor more than 30%, no more than 40%, or no more than 50%on average, distributed binomially. In some embodiments, the nuclease ofinterest is a Cas9 nuclease, a zinc finger nuclease, a TALEN, a homingendonuclease, an organic compound nuclease, or an enediyne antibiotic(e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin,bleomycin). In some embodiments, the candidate nuclease target sites areCas9 nuclease target sites that comprise a [sgRNA-complementarysequence]-[PAM] structure, wherein the sgRNA-complementary sequencecomprises 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,25, 26, 27, 28, 29, or 30 nucleotides.

Some aspects of this disclosure provide methods for selecting a nucleasethat specifically cuts a consensus target site from a plurality ofnucleases. In some embodiments, the method comprises (a) providing aplurality of candidate nucleases that cut the same consensus sequence;(b) for each of the candidate nucleases of step (a), identifying anuclease target site cleaved by the candidate nuclease that differ fromthe consensus target site using a method provided herein; (c) selectinga nuclease based on the nuclease target site(s) identified in step (b).In some embodiments, the nuclease selected in step (c) is the nucleasethat cleaves the consensus target site with the highest specificity. Insome embodiments, the nuclease that cleaves the consensus target sitewith the highest specificity is the candidate nuclease that cleaves thelowest number of target sites that differ from the consensus site. Insome embodiments, the candidate nuclease that cleaves the consensustarget site with the highest specificity is the candidate nuclease thatcleaves the lowest number of target sites that are different from theconsensus site in the context of a target genome. In some embodiments,the candidate nuclease selected in step (c) is a nuclease that does notcleave any target site other than the consensus target site. In someembodiments, the candidate nuclease selected in step (c) is a nucleasethat does not cleave any target site other than the consensus targetsite within the genome of a subject at a therapeutically effectiveconcentration of the nuclease. In some embodiments, the method furthercomprises contacting a genome with the nuclease selected in step (c). Insome embodiments, the genome is a vertebrate, mammalian, human,non-human primate, rodent, mouse, rat, hamster, goat, sheep, cattle,dog, cat, reptile, amphibian, fish, nematode, insect, or fly genome. Insome embodiments, the genome is within a living cell. In someembodiments, the genome is within a subject. In some embodiments, theconsensus target site is within an allele that is associated with adisease or disorder. In some embodiments, cleavage of the consensustarget site results in treatment or prevention of a disease or disorder,e.g., amelioration or prevention of at least one sign and/or symptom ofthe disease or disorder. In some embodiments, cleavage of the consensustarget site results in the alleviation of a sign and/or symptom of thedisease or disorder. In some embodiments, cleavage of the consensustarget site results in the prevention of the disease or disorder. Insome embodiments, the disease is HIV/AIDS. In some embodiments, theallele is a CCR5 allele. In some embodiments, the disease is aproliferative disease. In some embodiments, the disease is cancer. Insome embodiments, the allele is a VEGFA allele.

Some aspects of this disclosure provide isolated nucleases that havebeen selected according to a method provided herein. In someembodiments, the nuclease has been engineered to cleave a target sitewithin a genome. In some embodiments, the nuclease is a Cas9 nucleasecomprising an sgRNA that is complementary to the target site within thegenome. In some embodiments, the nuclease is a Zinc Finger Nuclease(ZFN) or a Transcription Activator-Like Effector Nuclease (TALEN), ahoming endonuclease, or an organic compound nuclease (e.g., an enediyne,an antibiotic nuclease, dynemicin, neocarzinostatin, calicheamicin,esperamicin, bleomycin, or a derivative thereof). In some embodiments,the nuclease has been selected based on cutting no other candidatetarget site, not more than one candidate target site, not more than twocandidate target sites, not more than three candidate target sites, notmore than four candidate target sites, not more than five candidatetarget sites, not more than six candidate target sites, not more thanseven candidate target sites, not more than eight candidate targetsites, not more than eight candidate target sites, not more than ninecandidate target sites, or not more than ten candidate target sites inaddition to its known nuclease target site.

Some aspects of this disclosure provide kits comprising a library ofnucleic acid molecules comprising candidate nuclease target sites asprovided herein. Some aspects of this disclosure provide kits comprisingan isolated nuclease as provided herein. In some embodiments, thenuclease is a Cas9 nuclease. In some embodiments, the kit furthercomprises a nucleic acid molecule comprising a target site of theisolated nuclease. In some embodiments, the kit comprises an excipientand instructions for contacting the nuclease with the excipient togenerate a composition suitable for contacting a nucleic acid with thenuclease. In some embodiments, the composition is suitable forcontacting a nucleic acid within a genome. In some embodiments, thecomposition is suitable for contacting a nucleic acid within a cell. Insome embodiments, the composition is suitable for contacting a nucleicacid within a subject. In some embodiments, the excipient is apharmaceutically acceptable excipient.

Some aspects of this disclosure provide pharmaceutical compositions thatare suitable for administration to a subject. In some embodiments, thecomposition comprises an isolated nuclease as provided herein. In someembodiments, the composition comprises a nucleic acid encoding such anuclease. In some embodiments, the composition comprises apharmaceutically acceptable excipient.

Other advantages, features, and uses of the invention will be apparentfrom the detailed description of certain non-limiting embodiments of theinvention; the drawings, which are schematic and not intended to bedrawn to scale; and the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

FIGS. 1A-B. In vitro selection overview. (a) Cas9 complexed with a shortguide RNA (sgRNA) recognizes ˜20 bases of a target DNA substrate that iscomplementary to the sgRNA sequence and cleaves both DNA strands. Thewhite triangles represent cleavage locations. (b) A modified version ofour previously described in vitro selection was used to comprehensivelyprofile Cas9 specificity. A concatemeric pre-selection DNA library inwhich each molecule contains one of 10¹² distinct variants of a targetDNA sequence (white rectangles) was generated from synthetic DNAoligonucleotides by ligation and rolling-circle amplification. Thislibrary was incubated with a Cas9:sgRNA complex of interest. Cleavedlibrary members contain 5′ phosphate groups (circles) and therefore aresubstrates for adapter ligation and PCR. The resulting amplicons weresubjected to high-throughput DNA sequencing and computational analysis.

FIGS. 2A-H. In vitro selection results for Cas9:CLTA1 sgRNA. Heat maps²¹show the specificity profiles of Cas9:CLTA1 sgRNA v2.1 underenzyme-limiting conditions (a, b), Cas9:CLTA1 sgRNA v1.0 underenzyme-saturating conditions (c, d), and Cas9:CLTA1 sgRNA v2.1 underenzyme-saturating conditions (e, f). Heat maps show all post-selectionsequences (a, c, e) or only those sequences containing a single mutationin the 20-base pair sgRNA-specified target site and two-base pair PAM(b, d, f). Specificity scores of 1.0 and −1.0 corresponds to 100%enrichment for and against, respectively, a particular base pair at aparticular position. Black boxes denote the intended target nucleotides.(g) Effect of Cas9:sgRNA concentration on specificity. Positionalspecificity changes between enzyme-limiting (200 nM DNA, 100 nMCas9:sgRNA v2.1) and enzyme-saturating (200 nM DNA, 1000 nM Cas9:sgRNAv2.1) conditions, normalized to the maximum possible change inpositional specificity, are shown for CLTA1. (h) Effect of sgRNAarchitecture on specificity. Positional specificity changes betweensgRNA v1.0 and sgRNA v2.1 under enzyme-saturating conditions, normalizedto the maximum possible change in positional specificity, are shown forCLTA1. See FIGS. 6-8, 25, and 26 for corresponding data for CLTA2,CLTA3, and CLTA4.

FIGS. 3A-D. Target sites profiled in this study. (A) The 5′ end of thesgRNA has 20 nucleotides that are complementary to the target site. Thetarget site contains an NGG motif (PAM) adjacent to the region ofRNA:DNA complementarity. (B) Four human clathrin gene (CLTA) targetsites are shown. (C, D) Four human clathrin gene (CLTA) target sites areshown with sgRNAs. sgRNA v1.0 is shorter than sgRNA v2.1. The PAM isshown for each site. The non-PAM end of the target site corresponds tothe 5′ end of the sgRNA.

FIG. 4. Cas9:guide RNA cleavage of on-target DNA sequences in vitro.Discrete DNA cleavage assays on an approximately 1-kb linear substratewere performed with 200 nM on-target site and 100 nM Cas9:v1.0 sgRNA,100 nM Cas9:v2.1 sgRNA, 1000 nM Cas9:v1.0 sgRNA, and 1000 nM Cas9:v2.1sgRNA for each of four CLTA target sites. For CLTA1, CLTA2, and CLTA4,Cas9:v2.1 sgRNA shows higher activity than Cas9:v1.0 sgRNA. For CLTA3,the activities of the Cas9:v1.0 sgRNA and Cas9:v2.1 sgRNA werecomparable.

FIGS. 5A-E. In vitro selection results for four target sites. In vitroselections were performed on 200 nM pre-selection library with 100 nMCas9:sgRNA v2.1, 1000 nM Cas9:sgRNA v1.0, or 1000 nM Cas9:sgRNA v2.1.(A) Post-selection PCR products are shown for the 12 selectionsperformed. DNA containing 1.5 repeats were quantified for each selectionand pooled in equimolar amounts before gel purification and sequencing.(B-E) Distributions of mutations are shown for pre-selection (black) andpost-selection libraries (colored). The post-selection libraries areenriched for sequences with fewer mutations than the pre-selectionlibraries. Mutations are counted from among the 20 base pairs specifiedby the sgRNA and the two-base pair PAM. P-values are <0.01 for allpairwise comparisons between distributions in each panel. P-values werecalculated using t-tests, assuming unequal size and unequal variance.

FIGS. 6A-F. In vitro selection results for Cas9:CLTA2 sgRNA. Heat maps²⁴show the specificity profiles of Cas9:CLTA2 sgRNA v2.1 underenzyme-limiting conditions (A, B), Cas9:CLTA2 sgRNA v1.0 underenzyme-excess conditions (C, D), and Cas9:CLTA2 sgRNA v2.1 underenzyme-excess conditions (E, F). Heat maps show all post-selectionsequences (A, C, E) or only those sequences containing a single mutationin the 20-base pair sgRNA-specified target site and two-base pair PAM(B, D, F). Specificity scores of 1.0 and −1.0 corresponds to 100%enrichment for and against, respectively, a particular base pair at aparticular position. Black boxes denote the intended target nucleotides.

FIGS. 7A-F. In vitro selection results for Cas9:CLTA3 sgRNA. Heat maps²⁴show the specificity profiles of Cas9:CLTA3 sgRNA v2.1 underenzyme-limiting conditions (A, B), Cas9:CLTA3 sgRNA v1.0 underenzyme-excess conditions (C, D), and Cas9:CLTA3 sgRNA v2.1 underenzyme-saturating conditions (E, F). Heat maps show all post-selectionsequences (A, C, E) or only those sequences containing a single mutationin the 20-base pair sgRNA-specified target site and two-base pair PAM(B, D, F). Specificity scores of 1.0 and −1.0 corresponds to 100%enrichment for and against, respectively, a particular base pair at aparticular position. Black boxes denote the intended target nucleotides.

FIGS. 8A-F. In vitro selection results for Cas9:CLTA4 sgRNA. Heat maps²⁴show the specificity profiles of Cas9:CLTA4 sgRNA v2.1 underenzyme-limiting conditions (A, B), Cas9:CLTA4 sgRNA v1.0 underenzyme-excess conditions (C, D), and Cas9:CLTA4 sgRNA v2.1 underenzyme-saturating conditions (E, F). Heat maps show all post-selectionsequences (A, C, E) or only those sequences containing a single mutationin the 20-base pair sgRNA-specified target site and two-base pair PAM(B, D, F). Specificity scores of 1.0 and −1.0 corresponds to 100%enrichment for and against, respectively, a particular base pair at aparticular position. Black boxes denote the intended target nucleotides.

FIGS. 9A-D. In vitro selection results as sequence logos. Informationcontent is plotted²⁵ for each target site position (1-20) specified byCLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) sgRNA v2.1 underenzyme-limiting conditions. Positions in the PAM are labelled “P1,”“P2,” and “P3.” Information content is plotted in bits. 2.0 bitsindicates absolute specificity and 0 bits indicates no specificity.

FIGS. 10A-L. Tolerance of mutations distal to the PAM for CLTA1. Themaximum specificity scores at each position are shown for the Cas9:CLTA1v2.1 sgRNA selections when considering only those sequences withon-target base pairs in gray, while allowing mutations in the first 1-12base pairs (a-l). The positions that are not constrained to on-targetbase pairs are indicated by dark bars. Higher specificity score valuesindicate higher specificity at a given position. The positions that werenot allowed to contain any mutations (gray) were plotted with aspecificity score of +1. For all panels, specificity scores werecalculated from pre-selection library sequences and post-selectionlibrary sequences with an n≧5,130 and n≧74,538, respectively.

FIGS. 11A-L. Tolerance of mutations distal to the PAM for CLTA2. Themaximum specificity scores at each position are shown for the Cas9:CLTA2v2.1 sgRNA selections when considering only those sequences withon-target base pairs in gray, while allowing mutations in the first 1-12base pairs (a-l). The positions that are not constrained to on-targetbase pairs are indicated by dark bars. Higher specificity score valuesindicate higher specificity at a given position. The positions that werenot allowed to contain any mutations (gray) were plotted with aspecificity score of +1. For all panels, specificity scores werecalculated from pre-selection library sequences and post-selectionlibrary sequences with an n≧3,190 and n≧25,365, respectively.

FIGS. 12A-L. Tolerance of mutations distal to the PAM for CLTA3. Themaximum specificity scores at each position are shown for the Cas9:CLTA3v2.1 sgRNA selections when considering only those sequences withon-target base pairs in gray, while allowing mutations in the first 1-12base pairs (a-l). The positions that are not constrained to on-targetbase pairs are indicated by dark bars. Higher specificity score valuesindicate higher specificity at a given position. The positions that werenot allowed to contain any mutations (gray) were plotted with aspecificity score of +1. For all panels, specificity scores werecalculated from pre-selection library sequences and post-selectionlibrary sequences with an n≧5,604 and n≧158,424, respectively.

FIGS. 13A-I. Tolerance of mutations distal to the PAM for CLTA4. Themaximum specificity scores at each position are shown for the Cas9:CLTA4v2.1 sgRNA selections when considering only those sequences withon-target base pairs in gray, while allowing mutations in the first 1-12base pairs (a-i). The positions that are not constrained to on-targetbase pairs are indicated by dark bars. Higher specificity score valuesindicate higher specificity at a given position. The positions that werenot allowed to contain any mutations (gray) were plotted with aspecificity score of +1. For all panels, specificity scores werecalculated from pre-selection library sequences and post-selectionlibrary sequences with an n≧2,323 and n≧21,819, respectively.

FIGS. 14A-L. Tolerance of mutations distal to the PAM in CLTA1 targetsites. Distributions of mutations are shown for in vitro selection on200 nM pre-selection library with 1000 nM Cas9:CLTA1 sgRNA v2.1. Thenumber of mutations shown are in a 1-12 base pair target sitesubsequence farthest from the PAM (a-l) when the rest of the targetsite, including the PAM, contains only on-target base pairs. Thepre-selection and post-selection distributions are similar for up tothree base pairs, demonstrating tolerance for target sites withmutations in the three base pairs farthest from the PAM when the rest ofthe target sites have optimal interactions with the Cas9:sgRNA. For allpanels, graphs were generated from pre-selection library sequences andpost-selection library sequences with an n≧5,130 and n≧74,538,respectively.

FIGS. 15A-L. Tolerance of mutations distal to the PAM in CLTA2 targetsites. Distributions of mutations are shown for in vitro selection on200 nM pre-selection library with 1000 nM Cas9:CLTA2 sgRNA v2.1. Thenumber of mutations shown are in a 1-12 base pair target sitesubsequence farthest from the PAM (a-l) when the rest of the targetsite, including the PAM, contains only on-target base pairs. Thepre-selection and post-selection distributions are similar for up tothree base pairs, demonstrating tolerance for target sites withmutations in the three base pairs farthest from the PAM when the rest ofthe target sites have optimal interactions with the Cas9:sgRNA. For allpanels, graphs were generated from pre-selection library sequences andpost-selection library sequences with an n≧3,190 and n≧21,265,respectively.

FIGS. 16A-L. Tolerance of mutations distal to PAM in CLTA3 target sites.Distributions of mutations are shown for in vitro selection on 200 nMpre-selection library with 1000 nM Cas9:CLTA3 sgRNA v2.1. The number ofmutations shown are in a 1-12 base pair target site subsequence farthestfrom the PAM (a-l) when the rest of the target site, including the PAM,contains only on-target base pairs. The pre-selection and post-selectiondistributions are similar for up to three base pairs, demonstratingtolerance for target sites with mutations in the three base pairsfarthest from the PAM when the rest of the target sites have optimalinteractions with the Cas9:sgRNA. For all panels, graphs were generatedfrom pre-selection library sequences and post-selection librarysequences with an n≧5,604 and n≧158,424, respectively.

FIGS. 17A-L. Tolerance of mutations distal to PAM in CLTA4 target sites.Distributions of mutations are shown for in vitro selection on 200 nMpre-selection library with 1000 nM Cas9:CLTA4 sgRNA v2.1. The number ofmutations shown are in a 1-12 base pair target site subsequence farthestfrom the PAM (a-l) when the rest of the target site, including the PAM,contains only on-target base pairs. The pre-selection and post-selectiondistributions are similar for up to three base pairs, demonstratingtolerance for target sites with mutations in the three base pairsfarthest from the PAM when the rest of the target sites have optimalinteractions with the Cas9:sgRNA. For all panels, graphs were generatedfrom pre-selection library sequences and post-selection librarysequences with an n≧2,323 and n≧21,819, respectively.

FIGS. 18A-D. Positional specificity patterns for 100 nM Cas9:sgRNA v2.1.Positional specificity, defined as the sum of the magnitude of thespecificity score for each of the four possible base pairs recognized ata certain position in the target site, is plotted for each target siteunder enzyme-limiting conditions for sgRNA v2.1 (A-D). The positionalspecificity is shown as a value normalized to the maximum positionalspecificity value of the target site. Positional specificity is highestat the end of the target site proximal to the PAM and is lowest in themiddle of the target site and in the several nucleotides most distal tothe PAM.

FIGS. 19A-D. Positional specificity patterns for 1000 nM Cas9:sgRNAv1.0. Positional specificity, defined as the sum of the magnitude of thespecificity score for each of the four possible base pairs recognized ata certain position in the target site, is plotted for each target siteunder enzyme-excess conditions with sgRNA v1.0 (A-D). The positionalspecificity is shown as a value normalized to the maximum positionalspecificity value of the target site. Positional specificity isrelatively constant across the target site but is lowest in the middleof the target site and in the several nucleotides most distal to thePAM.

FIGS. 20A-D. Positional specificity patterns for 1000 nM Cas9:sgRNAv2.1. Positional specificity, defined as the sum of the magnitude of thespecificity score for each of the four possible base pairs recognized ata certain position in the target site, is plotted for each target siteunder enzyme-excess conditions with sgRNA v2.1 (A-D). The positionalspecificity is shown as a value normalized to the maximum positionalspecificity value of the target site. Positional specificity isrelatively constant across the target site but is lowest in the middleof the target site and in the several nucleotides most distal to thePAM.

FIGS. 21A-D. PAM nucleotide preferences. The abundance in thepre-selection library and post-selection libraries under enzyme-limitingor enzyme-excess conditions are shown for all 16 possible PAMdinucleotides for selections with CLTA1 (a), CLTA2 (b), CLTA3 (c), andCLTA4 (d) sgRNA v2.1. GG dinucleotides increased in abundance in thepost-selection libraries, while the other possible PAM dinucleotidesdecreased in abundance after the selection.

FIGS. 22A-D. PAM nucleotide preferences for on-target sites. Onlypost-selection library members containing no mutations in the 20 basepairs specified by the guide RNAs were included in this analysis. Theabundance in the pre-selection library and post-selection librariesunder enzyme-limiting and enzyme-excess conditions are shown for all 16possible PAM dinucleotides for selections with CLTA1 (A), CLTA2 (B),CLTA3 (C), and CLTA4 (D) sgRNA v2.1. GG dinucleotides increased inabundance in the post-selection libraries, while the other possible PAMdinucleotides generally decreased in abundance after the selection,although this effect for the enzyme-excess concentrations of Cas9:sgRNAwas modest or non-existent for many dinucleotides.

FIGS. 23A-D. PAM dinucleotide specificity scores. The specificity scoresunder enzyme-limiting and enzyme-excess conditions are shown for all 16possible PAM dinucleotides (positions 2 and 3 of the three-nucleotideNGG PAM) for selections with CLTA1 (A), CLTA2 (B), CLTA3 (C), and CLTA4(D) sgRNA v2.1. The specificity score indicates the enrichment of thePAM dinucleotide in the post-selection library relative to thepre-selection library, normalized to the maximum possible enrichment ofthat dinucleotide. A specificity score of +1.0 indicates that adinucleotide is 100% enriched in the post-selection library, and aspecificity score of −1.0 indicates that a dinucleotide is 100%de-enriched. GG dinucleotides were the most enriched in thepost-selection libraries, and AG, GA, GC, GT, and TG show less relativede-enrichment compared to the other possible PAM dinucleotides.

FIGS. 24A-D. PAM dinucleotide specificity scores for on-target sites.Only post-selection library members containing no mutations in the 20base pairs specified by the guide RNAs were included in this analysis.The specificity scores under enzyme-limiting and enzyme-excessconditions are shown for all 16 possible PAM dinucleotides (positions 2and 3 of the three-nucleotide NGG PAM) for selections with CLTA1 (A),CLTA2 (B), CLTA3 (C), and CLTA4 (D) sgRNA v2.1. The specificity scoreindicates the enrichment of the PAM dinucleotide in the post-selectionlibrary relative to the pre-selection library, normalized to the maximumpossible enrichment of that dinucleotide. A specificity score of +1.0indicates that a dinucleotide is 100% enriched in the post-selectionlibrary, and a specificity score of −1.0 indicates that a dinucleotideis 100% de-enriched. GG dinucleotides were the most enriched in thepost-selection libraries, AG and GA nucleotides were neither enriched orde-enriched in at least one selection condition, and GC, GT, and TG showless relative de-enrichment compared to the other possible PAMdinucleotides.

FIGS. 25A-D. Effects of Cas9:sgRNA concentration on specificity.Positional specificity changes between enzyme-limiting (200 nM DNA, 100nM Cas9:sgRNA v2.1) and enzyme-excess (200 nM DNA, 1000 nM Cas9:sgRNAv2.1) conditions are shown for selections with sgRNAs targeting CLTA1(A), CLTA2 (B), CLTA3 (C), and CLTA4 (D) target sites. Lines indicatethe maximum possible change in positional specificity for a givenposition. The highest changes in specificity occur proximal to the PAMas enzyme concentration is increased.

FIGS. 26A-D. Effects of sgRNA architecture on specificity. Positionalspecificity changes between Cas9:sgRNA v1.0 and Cas9:sgRNA v2.1 underenzyme-excess (200 nM DNA, 1000 nM Cas9:sgRNA v2.1) conditions are shownfor selections with sgRNAs targeting CLTA1 (A), CLTA2 (B), CLTA3 (C),and CLTA4 (D) target sites. Lines indicate the maximum possible changein positional specificity for a given position.

FIG. 27. Cas9:guide RNA cleavage of off-target DNA sequences in vitro.Discrete DNA cleavage assays on a 96-bp linear substrate were performedwith 200 nM DNA and 1000 nM Cas9:CLTA4 v2.1 sgRNA for the on-targetCLTA4 site (CLTA4-0) and five CLTA4 off-target sites identified by invitro selection. Enrichment values shown are from the in vitro selectionwith 1000 nM Cas9:CLTA4 v2.1 sgRNA. CLTA4-1 and CLTA4-3 were the mosthighly enriched sequences under these conditions. CLTA4-2a, CLTA4-2b,and CLTA4-2c are two-mutation sequences that represent a range ofenrichment values from high enrichment to no enrichment to highde-enrichment. Lowercase letters indicate mutations relative to theon-target CLTA4 site. The enrichment values are qualitatively consistentwith the observed amount of cleavage in vitro.

FIG. 28. Effect of guide RNA architecture and Cas9:sgRNA concentrationon in vitro cleavage of an off-target site. Discrete DNA cleavage assayson a 96-bp linear substrate were performed with 200 nM DNA and 100 nMCas9:v1.0 sgRNA, 100 nM Cas9:v2.1 sgRNA, 1000 nM Cas9:v1.0 sgRNA, or1000 nM Cas9:v2.1 sgRNA for the CLTA4-3 off-target site (5′GggGATGTAGTGTTTCCACtGGG—mutations are shown in lowercase letters). DNAcleavage is observed under all four conditions tested, and cleavagerates are higher under enzyme-excess conditions, or with v2.1 sgRNAcompared with v1.0 sgRNA.

DEFINITIONS

As used herein and in the claims, the singular forms “a,” “an,” and“the” include the singular and the plural reference unless the contextclearly indicates otherwise. Thus, for example, a reference to “anagent” includes a single agent and a plurality of such agents.

The term “Cas9” or “Cas9 nuclease” refers to an RNA-guided nucleasecomprising a Cas9 protein, or a fragment thereof. A Cas9 nuclease isalso referred to sometimes as a casnl nuclease or a CRISPR (clusteredregularly interspaced short palindromic repeat)-associated nuclease.CRISPR is an adaptive immune system that provides protection againstmobile genetic elements (e.g., viruses, transposable elements andconjugative plasmids). CRISPR clusters contain spacers, sequencescomplementary to antecedent mobile elements, and target invading nucleicacids. CRISPR clusters are transcribed and processed into CRISPR RNA(crRNA). In type II CRISPR systems correct processing of pre-crRNArequires a trans-encoded small RNA (tracrRNA), endogenous ribonuclease 3(rnc) and a Cas9 protein. The tracrRNA serves as a guide forribonuclease 3-aided processing of pre-crRNA. Subsequently,Cas9/crRNA/tracrRNA endonucleolytically cleaves linear or circular dsDNAtarget complementary to the spacer. The target strand not complementaryto crRNA is first cut endonucleolytically, then trimmed 3′-5′exonucleolytically. In nature, DNA-binding and cleavage typicallyrequires protein and both RNA species. However, single guide RNAs(“sgRNA”, or simply “gNRA”) can be engineered so as to incorporateaspects of both the crRNA and tracrRNA into a single RNA molecule. See,e.g., Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J. A.,Charpentier E. Science 337:816-821(2012), the entire contents of whichis hereby incorporated by reference. Cas9 recognizes a short motif inthe CRISPR repeat sequences (the PAM or protospacer adjacent motif) tohelp distinguish self versus non-self. Cas9 nuclease sequences andstructures are well known to those of skill in the art (see, e.g.,“Complete genome sequence of an M1 strain of Streptococcus pyogenes.”Ferretti J. J., McShan W. M., Ajdic D. J., Savic D. J., Savic G., LyonK., Primeaux C., Sezate S., Suvorov A. N., Kenton S., Lai H. S., Lin S.P., Qian Y., Jia H. G., Najar F. Z., Ren Q., Zhu H., Song L.expand/collapse author list McLaughlin R. E., Proc. Natl. Acad. Sci.U.S.A. 98:4658-4663(2001); “CRISPR RNA maturation by trans-encoded smallRNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C.M., Gonzales K., Chao Y., Pirzada Z. A., Eckert M. R., Vogel J.,Charpentier E., Nature 471:602-607(2011); and “A programmabledual-RNA-guided DNA endonuclease in adaptive bacterial immunity.” JinekM., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E.Science 337:816-821(2012), the entire contents of each of which areincorporated herein by reference). Cas9 orthologs have been described invarious species, including, but not limited to, S. pyogenes and S.thermophilus. Additional suitable Cas9 nucleases and sequences will beapparent to those of skill in the art based on this disclosure, and suchCas9 nucleases and sequences include Cas9 sequences from the organismsand loci disclosed in Chylinski, Rhun, and Charpentier, “The tracrRNAand Cas9 families of type II CRISPR-Cas immunity systems” (2013) RNABiology 10:5, 726-737; the entire contents of which are incorporatedherein by reference. In some embodiments, proteins comprising Cas9 orfragments thereof proteins are referred to as “Cas9 variants.” A Cas9variant shares homology to Cas9, or a fragment thereof. For example aCas9 variant is at least about 70% identical, at least about 80%identical, at least about 90% identical, at least about 95% identical,at least about 98% identical, at least about 99% identical, at leastabout 99.5% identical, or at least about 99.9% to wild type Cas9. Insome embodiments, the Cas9 variant comprises a fragment of Cas9 (e.g., agRNA binding domain or a DNA-cleavage domain), such that the fragment isat least about 70% identical, at least about 80% identical, at leastabout 90% identical, at least about 95% identical, at least about 98%identical, at least about 99% identical, at least about 99.5% identical,or at least about 99.9% to the corresponding fragment of wild type Cas9.In some embodiments, wild type Cas9 corresponds to Cas9 fromStreptococcus pyogenes (NCBI Reference Sequence: NC_(—)017053.1, SEQ IDNO:40 (nucleotide); SEQ ID NO:41 (amino acid)).

(SEQ ID NO: 40) ATGGATAAGAAATACTCAATAGGCTTAGATATCGGCACAAATAGCGTCGGATGGGCGGTGATCACTGATGATTATAAGGTTCCGTCTAAAAAGTTCAAGGTTCTGGGAAATACAGACCGCCACAGTATCAAAAAAAATCTTATAGGGGCTCTTTTATTTGGCAGTGGAGAGACAGCGGAAGCGACTCGTCTCAAACGGACAGCTCGTAGAAGGTATACACGTCGGAAGAATCGTATTTGTTATCTACAGGAGATTTTTTCAAATGAGATGGCGAAAGTAGATGATAGTTTCTTTCATCGACTTGAAGAGTCTTTTTTGGTGGAAGAAGACAAGAAGCATGAACGTCATCCTATTTTTGGAAATATAGTAGATGAAGTTGCTTATCATGAGAAATATCCAACTATCTATCATCTGCGAAAAAAATTGGCAGATTCTACTGATAAAGCGGATTTGCGCTTAATCTATTTGGCCTTAGCGCATATGATTAAGTTTCGTGGTCATTTTTTGATTGAGGGAGATTTAAATCCTGATAATAGTGATGTGGACAAACTATTTATCCAGTTGGTACAAATCTACAATCAATTATTTGAAGAAAACCCTATTAACGCAAGTAGAGTAGATGCTAAAGCGATTCTTTCTGCACGATTGAGTAAATCAAGACGATTAGAAAATCTCATTGCTCAGCTCCCCGGTGAGAAGAGAAATGGCTTGTTTGGGAATCTCATTGCTTTGTCATTGGGATTGACCCCTAATTTTAAATCAAATTTTGATTTGGCAGAAGATGCTAAATTACAGCTTTCAAAAGATACTTACGATGATGATTTAGATAATTTATTGGCGCAAATTGGAGATCAATATGCTGATTTGTTTTTGGCAGCTAAGAATTTATCAGATGCTATTTTACTTTCAGATATCCTAAGAGTAAATAGTGAAATAACTAAGGCTCCCCTATCAGCTTCAATGATTAAGCGCTACGATGAACATCATCAAGACTTGACTCTTTTAAAAGCTTTAGTTCGACAACAACTTCCAGAAAAGTATAAAGAAATCTTTTTTGATCAATCAAAAAACGGATATGCAGGTTATATTGATGGGGGAGCTAGCCAAGAAGAATTTTATAAATTTATCAAACCAATTTTAGAAAAAATGGATGGTACTGAGGAATTATTGGTGAAACTAAATCGTGAAGATTTGCTGCGCAAGCAACGGACCTTTGACAACGGCTCTATTCCCCATCAAATTCACTTGGGTGAGCTGCATGCTATTTTGAGAAGACAAGAAGACTTTTATCCATTTTTAAAAGACAATCGTGAGAAGATTGAAAAAATCTTGACTTTTCGAATTCCTTATTATGTTGGTCCATTGGCGCGTGGCAATAGTCGTTTTGCATGGATGACTCGGAAGTCTGAAGAAACAATTACCCCATGGAATTTTGAAGAAGTTGTCGATAAAGGTGCTTCAGCTCAATCATTTATTGAACGCATGACAAACTTTGATAAAAATCTTCCAAATGAAAAAGTACTACCAAAACATAGTTTGCTTTATGAGTATTTTACGGTTTATAACGAATTGACAAAGGTCAAATATGTTACTGAGGGAATGCGAAAACCAGCATTTCTTTCAGGTGAACAGAAGAAAGCCATTGTTGATTTACTCTTCAAAACAAATCGAAAAGTAACCGTTAAGCAATTAAAAGAAGATTATTTCAAAAAAATAGAATGTTTTGATAGTGTTGAAATTTCAGGAGTTGAAGATAGATTTAATGCTTCATTAGGCGCCTACCATGATTTGCTAAAAATTATTAAAGATAAAGATTTTTTGGATAATGAAGAAAATGAAGATATCTTAGAGGATATTGTTTTAACATTGACCTTATTTGAAGATAGGGGGATGATTGAGGAAAGACTTAAAACATATGCTCACCTCTTTGATGATAAGGTGATGAAACAGCTTAAACGTCGCCGTTATACTGGTTGGGGACGTTTGTCTCGAAAATTGATTAATGGTATTAGGGATAAGCAATCTGGCAAAACAATATTAGATTTTTTGAAATCAGATGGTTTTGCCAATCGCAATTTTATGCAGCTGATCCATGATGATAGTTTGACATTTAAAGAAGATATTCAAAAAGCACAGGTGTCTGGACAAGGCCATAGTTTACATGAACAGATTGCTAACTTAGCTGGCAGTCCTGCTATTAAAAAAGGTATTTTACAGACTGTAAAAATTGTTGATGAACTGGTCAAAGTAATGGGGCATAAGCCAGAAAATATCGTTATTGAAATGGCACGTGAAAATCAGACAACTCAAAAGGGCCAGAAAAATTCGCGAGAGCGTATGAAACGAATCGAAGAAGGTATCAAAGAATTAGGAAGTCAGATTCTTAAAGAGCATCCTGTTGAAAATACTCAATTGCAAAATGAAAAGCTCTATCTCTATTATCTACAAAATGGAAGAGACATGTATGTGGACCAAGAATTAGATATTAATCGTTTAAGTGATTATGATGTCGATCACATTGTTCCACAAAGTTTCATTAAAGACGATTCAATAGACAATAAGGTACTAACGCGTTCTGATAAAAATCGTGGTAAATCGGATAACGTTCCAAGTGAAGAAGTAGTCAAAAAGATGAAAAACTATTGGAGACAACTTCTAAACGCCAAGTTAATCACTCAACGTAAGTTTGATAATTTAACGAAAGCTGAACGTGGAGGTTTGAGTGAACTTGATAAAGCTGGTTTTATCAAACGCCAATTGGTTGAAACTCGCCAAATCACTAAGCATGTGGCACAAATTTTGGATAGTCGCATGAATACTAAATACGATGAAAATGATAAACTTATTCGAGAGGTTAAAGTGATTACCTTAAAATCTAAATTAGTTTCTGACTTCCGAAAAGATTTCCAATTCTATAAAGTACGTGAGATTAACAATTACCATCATGCCCATGATGCGTATCTAAATGCCGTCGTTGGAACTGCTTTGATTAAGAAATATCCAAAACTTGAATCGGAGTTTGTCTATGGTGATTATAAAGTTTATGATGTTCGTAAAATGATTGCTAAGTCTGAGCAAGAAATAGGCAAAGCAACCGCAAAATATTTCTTTTACTCTAATATCATGAACTTCTTCAAAACAGAAATTACACTTGCAAATGGAGAGATTCGCAAACGCCCTCTAATCGAAACTAATGGGGAAACTGGAGAAATTGTCTGGGATAAAGGGCGAGATTTTGCCACAGTGCGCAAAGTATTGTCCATGCCCCAAGTCAATATTGTCAAGAAAACAGAAGTACAGACAGGCGGATTCTCCAAGGAGTCAATTTTACCAAAAAGAAATTCGGACAAGCTTATTGCTCGTAAAAAAGACTGGGATCCAAAAAAATATGGTGGTTTTGATAGTCCAACGGTAGCTTATTCAGTCCTAGTGGTTGCTAAGGTGGAAAAAGGGAAATCGAAGAAGTTAAAATCCGTTAAAGAGTTACTAGGGATCACAATTATGGAAAGAAGTTCCTTTGAAAAAAATCCGATTGACTTTTTAGAAGCTAAAGGATATAAGGAAGTTAAAAAAGACTTAATCATTAAACTACCTAAATATAGTCTTTTTGAGTTAGAAAACGGTCGTAAACGGATGCTGGCTAGTGCCGGAGAATTACAAAAAGGAAATGAGCTGGCTCTGCCAAGCAAATATGTGAATTTTTTATATTTAGCTAGTCATTATGAAAAGTTGAAGGGTAGTCCAGAAGATAACGAACAAAAACAATTGTTTGTGGAGCAGCATAAGCATTATTTAGATGAGATTATTGAGCAAATCAGTGAATTTTCTAAGCGTGTTATTTTAGCAGATGCCAATTTAGATAAAGTTCTTAGTGCATATAACAAACATAGAGACAAACCAATACGTGAACAAGCAGAAAATATTATTCATTTATTTACGTTGACGAATCTTGGAGCTCCCGCTGCTTTTAAATATTTTGATACAACAATTGATCGTAAACGATATACGTCTACAAAAGAAGTTTTAGATGCCACTCTTATCCATCAATCCATCACTGGTCTTTATGAAACACGCATTGATTTGAGTCAGCTAGGAGGTGA CTGA (SEQ ID NO: 41)MDKKYSIGLDIGTNSVGWAVITDDYKVPSKKFKVLGNTDRHSIKKNLIGALLFGSGETAEATRLKRTARRRYTRRKNRICYLQEIFSNEMAKVDDSFFHRLEESFLVEEDKKHERHPIFGNIVDEVAYHEKYPTIYHLRKKLADSTDKADLRLIYLALAHMIKFRGHFLIEGDLNPDNSDVDKLFIQLVQIYNQLFEENPINASRVDAKAILSARLSKSRRLENLIAQLPGEKRNGLFGNLIALSLGLTPNFKSNFDLAEDAKLQLSKDTYDDDLDNLLAQIGDQYADLFLAAKNLSDAILLSDILRVNSEITKAPLSASMIKRYDEHHQDLTLLKALVRQQLPEKYKEIFFDQSKNGYAGYIDGGASQEEFYKFIKPILEKMDGTEELLVKLNREDLLRKQRTFDNGSIPHQIHLGELHAILRRQEDFYPFLKDNREKIEKILTFRIPYYVGPLARGNSRFAWMTRKSEETITPWNFEEVVDKGASAQSFIERMTNFDKNLPNEKVLPKHSLLYEYFTVYNELTKVKYVTEGMRKPAFLSGEQKKAIVDLLFKTNRKVTVKQLKEDYFKKIECFDSVEISGVEDRFNASLGAYHDLLKIIKDKDFLDNEENEDILEDIVLTLTLFEDRGMIEERLKTYAHLFDDKVMKQLKRRRYTGWGRLSRKLINGIRDKQSGKTILDFLKSDGFANRNFMQLIHDDSLTFKEDIQKAQVSGQGHSLHEQIANLAGSPAIKKGILQTVKIVDELVKVMGHKPENIVIEMARENQTTQKGQKNSRERMKRIEEGIKELGSQILKEHPVENTQLQNEKLYLYYLQNGRDMYVDQELDINRLSDYDVDHIVPQSFIKDDSIDNKVLTRSDKNRGKSDNVPSEEVVKKMKNYWRQLLNAKLITQRKFDNLTKAERGGLSELDKAGFIKRQLVETRQITKHVAQILDSRMNTKYDENDKLIREVKVITLKSKLVSDFRKDFQFYKVREINNYHHAHDAYLNAVVGTALIKKYPKLESEFVYGDYKVYDVRKMIAKSEQEIGKATAKYFFYSNIMNFFKTEITLANGEIRKRPLIETNGETGEIVWDKGRDFATVRKVLSMPQVNIVKKTEVQTGGFSKESILPKRNSDKLIARKKDWDPKKYGGFDSPTVAYSVLVVAKVEKGKSKKLKSVKELLGITIMERSSFEKNPIDFLEAKGYKEVKKDLIIKLPKYSLFELENGRKRMLASAGELQKGNELALPSKYVNFLYLASHYEKLKGSPEDNEQKQLFVEQHKHYLDEIIEQISEFSKRVILADANLDKVLSAYNKHRDKPIREQAENIIHLFTLTNLGAPAAFKYFDTTIDRKRYTSTKEVLDATLIHQS ITGLYETRIDLSQLGGD

The term “concatemer,” as used herein in the context of nucleic acidmolecules, refers to a nucleic acid molecule that contains multiplecopies of the same DNA sequences linked in a series. For example, aconcatemer comprising ten copies of a specific sequence of nucleotides(e.g., [XYZ]₁₀), would comprise ten copies of the same specific sequencelinked to each other in series, e.g.,5′-XYZXYZXYZXYZXYZXYZXYZXYZXYZXYZ-3′. A concatemer may comprise anynumber of copies of the repeat unit or sequence, e.g., at least 2copies, at least 3 copies, at least 4 copies, at least 5 copies, atleast 10 copies, at least 100 copies, at least 1000 copies, etc. Anexample of a concatemer of a nucleic acid sequence comprising a nucleasetarget site and a constant insert sequence would be [(targetsite)-(constant insert sequence)]₃₀₀. A concatemer may be a linearnucleic acid molecule, or may be circular.

The terms “conjugating,” “conjugated,” and “conjugation” refer to anassociation of two entities, for example, of two molecules such as twoproteins, two domains (e.g., a binding domain and a cleavage domain), ora protein and an agent, e.g., a protein binding domain and a smallmolecule. In some aspects, the association is between a protein (e.g.,RNA-programmable nuclease) and a nucleic acid (e.g., a guide RNA). Theassociation can be, for example, via a direct or indirect (e.g., via alinker) covalent linkage or via non-covalent interactions. In someembodiments, the association is covalent. In some embodiments, twomolecules are conjugated via a linker connecting both molecules. Forexample, in some embodiments where two proteins are conjugated to eachother, e.g., a binding domain and a cleavage domain of an engineerednuclease, to form a protein fusion, the two proteins may be conjugatedvia a polypeptide linker, e.g., an amino acid sequence connecting theC-terminus of one protein to the N-terminus of the other protein.

The term “consensus sequence,” as used herein in the context of nucleicacid sequences, refers to a calculated sequence representing the mostfrequent nucleotide residues found at each position in a plurality ofsimilar sequences. Typically, a consensus sequence is determined bysequence alignment in which similar sequences are compared to each otherand similar sequence motifs are calculated. In the context of nucleasetarget site sequences, a consensus sequence of a nuclease target sitemay, in some embodiments, be the sequence most frequently bound, orbound with the highest affinity, by a given nuclease. With respect toRNA-programmable nuclease (e.g., Cas9) target site sequences, theconsensus sequence may, in some embodiments, be the sequence or regionto which a gRNA, or a plurality of gRNAs, is expected or designed tobind, e.g., based on complementary base pairing.

The term “effective amount,” as used herein, refers to an amount of abiologically active agent that is sufficient to elicit a desiredbiological response. For example, in some embodiments, an effectiveamount of a nuclease may refer to the amount of the nuclease that issufficient to induce cleavage of a target site specifically bound andcleaved by the nuclease. As will be appreciated by the skilled artisan,the effective amount of an agent, e.g., a nuclease, a hybrid protein, ora polynucleotide, may vary depending on various factors as, for example,on the desired biological response, the specific allele, genome, targetsite, cell, or tissue being targeted, and the agent being used.

The term “enediyne,” as used herein, refers to a class of bacterialnatural products characterized by either nine- and ten-membered ringscontaining two triple bonds separated by a double bond (see, e.g., K. C.Nicolaou; A. L. Smith; E. W. Yue (1993). “Chemistry and biology ofnatural and designed enediynes”. PNAS 90 (13): 5881-5888; the entirecontents of which are incorporated herein by reference). Some enediynesare capable of undergoing Bergman cyclization, and the resultingdiradical, a 1,4-dehydrobenzene derivative, is capable of abstractinghydrogen atoms from the sugar backbone of DNA which results in DNAstrand cleavage (see, e.g., S. Walker; R. Landovitz; W. D. Ding; G. A.Ellestad; D. Kahne (1992). “Cleavage behavior of calicheamicin gamma 1and calicheamicin T”. Proc Natl Acad Sci U.S.A. 89 (10): 4608-12; theentire contents of which are incorporated herein by reference). Theirreactivity with DNA confers an antibiotic character to many enediynes,and some enediynes are clinically investigated as anticancerantibiotics. Nonlimiting examples of enediynes are dynemicin,neocarzinostatin, calicheamicin, esperamicin (see, e.g., Adrian L. Smithand K. C. Bicolaou, “The Enediyne Antibiotics” J. Med. Chem., 1996, 39(11), pp 2103-2117; and Donald Borders, “Enediyne antibiotics asantitumor agents,” Informa Healthcare; 1^(st) edition (Nov. 23, 1994,ISBN-10: 0824789385; the entire contents of which are incorporatedherein by reference).

The term “homing endonuclease,” as used herein, refers to a type ofrestriction enzymes typically encoded by introns or inteins Edgell DR(February 2009). “Selfish DNA: homing endonucleases find a home”. CurrBiol 19 (3): R115-R117; Jasin M (June 1996). “Genetic manipulation ofgenomes with rare-cutting endonucleases”. Trends Genet 12 (6): 224-8;Burt A, Koufopanou V (December 2004). “Homing endonuclease genes: therise and fall and rise again of a selfish element”. Curr Opin Genet Dev14 (6): 609-15; the entire contents of which are incorporated herein byreference. Homing endonuclease recognition sequences are long enough tooccur randomly only with a very low probability (approximately onceevery 7×10¹⁰ bp), and are normally found in only one instance pergenome.

The term “library,” as used herein in the context of nucleic acids orproteins, refers to a population of two or more different nucleic acidsor proteins, respectively. For example, a library of nuclease targetsites comprises at least two nucleic acid molecules comprising differentnuclease target sites. In some embodiments, a library comprises at least10¹, at least 10², at least 10³, at least 10⁴, at least 10⁵, at least10⁶, at least 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least10¹¹, at least 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵different nucleic acids or proteins. In some embodiments, the members ofthe library may comprise randomized sequences, for example, fully orpartially randomized sequences. In some embodiments, the librarycomprises nucleic acid molecules that are unrelated to each other, e.g.,nucleic acids comprising fully randomized sequences. In otherembodiments, at least some members of the library may be related, forexample, they may be variants or derivatives of a particular sequence,such as a consensus target site sequence.

The term “linker,” as used herein, refers to a chemical group or amolecule linking two adjacent molecules or moieties, e.g., a bindingdomain and a cleavage domain of a nuclease. Typically, the linker ispositioned between, or flanked by, two groups, molecules, or othermoieties and connected to each one via a covalent bond, thus connectingthe two. In some embodiments, the linker is an amino acid or a pluralityof amino acids (e.g., a peptide or protein). In some embodiments, thelinker is an organic molecule, group, polymer, or chemical moiety.

The term “nuclease,” as used herein, refers to an agent, for example aprotein or a small molecule, capable of cleaving a phosphodiester bondconnecting nucleotide residues in a nucleic acid molecule. In someembodiments, a nuclease is a protein, e.g., an enzyme that can bind anucleic acid molecule and cleave a phosphodiester bond connectingnucleotide residues within the nucleic acid molecule. A nuclease may bean endonuclease, cleaving a phosphodiester bonds within a polynucleotidechain, or an exonuclease, cleaving a phosphodiester bond at the end ofthe polynucleotide chain. In some embodiments, a nuclease is asite-specific nuclease, binding and/or cleaving a specificphosphodiester bond within a specific nucleotide sequence, which is alsoreferred to herein as the “recognition sequence,” the “nuclease targetsite,” or the “target site.” In some embodiments, a nuclease is aRNA-guided (i.e., RNA-programmable) nuclease, which complexes with(e.g., binds with) an RNA having a sequence that complements a targetsite, thereby providing the sequence specificity of the nuclease. Insome embodiments, a nuclease recognizes a single stranded target site,while in other embodiments, a nuclease recognizes a double-strandedtarget site, for example a double-stranded DNA target site. The targetsites of many naturally occurring nucleases, for example, many naturallyoccurring DNA restriction nucleases, are well known to those of skill inthe art. In many cases, a DNA nuclease, such as EcoRI, HindIII, orBamHI, recognize a palindromic, double-stranded DNA target site of 4 to10 base pairs in length, and cut each of the two DNA strands at aspecific position within the target site. Some endonucleases cut adouble-stranded nucleic acid target site symmetrically, i.e., cuttingboth strands at the same position so that the ends comprise base-pairednucleotides, also referred to herein as blunt ends. Other endonucleasescut a double-stranded nucleic acid target sites asymmetrically, i.e.,cutting each strand at a different position so that the ends compriseunpaired nucleotides. Unpaired nucleotides at the end of adouble-stranded DNA molecule are also referred to as “overhangs,” e.g.,as “5′-overhang” or as “3′-overhang,” depending on whether the unpairednucleotide(s) form(s) the 5′ or the 3′ end of the respective DNA strand.Double-stranded DNA molecule ends ending with unpaired nucleotide(s) arealso referred to as sticky ends, as they can “stick to” otherdouble-stranded DNA molecule ends comprising complementary unpairednucleotide(s). A nuclease protein typically comprises a “binding domain”that mediates the interaction of the protein with the nucleic acidsubstrate, and also, in some cases, specifically binds to a target site,and a “cleavage domain” that catalyzes the cleavage of thephosphodiester bond within the nucleic acid backbone. In someembodiments a nuclease protein can bind and cleave a nucleic acidmolecule in a monomeric form, while, in other embodiments, a nucleaseprotein has to dimerize or multimerize in order to cleave a targetnucleic acid molecule. Binding domains and cleavage domains of naturallyoccurring nucleases, as well as modular binding domains and cleavagedomains that can be fused to create nucleases binding specific targetsites, are well known to those of skill in the art. For example, zincfingers or transcriptional activator like elements can be used asbinding domains to specifically bind a desired target site, and fused orconjugated to a cleavage domain, for example, the cleavage domain ofFokI, to create an engineered nuclease cleaving the target site.

The terms “nucleic acid” and “nucleic acid molecule,” as used herein,refer to a compound comprising a nucleobase and an acidic moiety, e.g.,a nucleoside, a nucleotide, or a polymer of nucleotides. Typically,polymeric nucleic acids, e.g., nucleic acid molecules comprising threeor more nucleotides are linear molecules, in which adjacent nucleotidesare linked to each other via a phosphodiester linkage. In someembodiments, “nucleic acid” refers to individual nucleic acid residues(e.g. nucleotides and/or nucleosides). In some embodiments, “nucleicacid” refers to an oligonucleotide chain comprising three or moreindividual nucleotide residues. As used herein, the terms“oligonucleotide” and “polynucleotide” can be used interchangeably torefer to a polymer of nucleotides (e.g., a string of at least threenucleotides). In some embodiments, “nucleic acid” encompasses RNA aswell as single and/or double-stranded DNA. Nucleic acids may benaturally occurring, for example, in the context of a genome, atranscript, an mRNA, tRNA, rRNA, siRNA, snRNA, a plasmid, cosmid,chromosome, chromatid, or other naturally occurring nucleic acidmolecule. On the other hand, a nucleic acid molecule may be anon-naturally occurring molecule, e.g., a recombinant DNA or RNA, anartificial chromosome, an engineered genome, or fragment thereof, or asynthetic DNA, RNA, DNA/RNA hybrid, or including non-naturally occurringnucleotides or nucleosides. Furthermore, the terms “nucleic acid,”“DNA,” “RNA,” and/or similar terms include nucleic acid analogs, i.e.analogs having other than a phosphodiester backbone. Nucleic acids canbe purified from natural sources, produced using recombinant expressionsystems and optionally purified, chemically synthesized, etc. Whereappropriate, e.g., in the case of chemically synthesized molecules,nucleic acids can comprise nucleoside analogs such as analogs havingchemically modified bases or sugars, and backbone modifications. Anucleic acid sequence is presented in the 5′ to 3′ direction unlessotherwise indicated. In some embodiments, a nucleic acid is or comprisesnatural nucleosides (e.g. adenosine, thymidine, guanosine, cytidine,uridine, deoxyadenosine, deoxythymidine, deoxyguanosine, anddeoxycytidine); nucleoside analogs (e.g., 2-aminoadenosine,2-thiothymidine, inosine, pyrrolo-pyrimidine, 3-methyl adenosine,5-methylcytidine, 2-aminoadenosine, C5-bromouridine, C5-fluorouridine,C5-iodouridine, C5-propynyl-uridine, C5-propynyl-cytidine,C5-methylcytidine, 2-aminoadenosine, 7-deazaadenosine, 7-deazaguanosine,8-oxoadenosine, 8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine);chemically modified bases; biologically modified bases (e.g., methylatedbases); intercalated bases; modified sugars (e.g., 2′-fluororibose,ribose, 2′-deoxyribose, arabinose, and hexose); and/or modifiedphosphate groups (e.g., phosphorothioates and 5′-N-phosphoramiditelinkages).

The term “pharmaceutical composition,” as used herein, refers to acomposition that can be administrated to a subject in the context oftreatment of a disease or disorder. In some embodiments, apharmaceutical composition comprises an active ingredient, e.g., anuclease or a nucleic acid encoding a nuclease, and a pharmaceuticallyacceptable excipient.

The term “proliferative disease,” as used herein, refers to any diseasein which cell or tissue homeostasis is disturbed in that a cell or cellpopulation exhibits an abnormally elevated proliferation rate.Proliferative diseases include hyperproliferative diseases, such aspre-neoplastic hyperplastic conditions and neoplastic diseases.Neoplastic diseases are characterized by an abnormal proliferation ofcells and include both benign and malignant neoplasias. Malignantneoplasia is also referred to as cancer.

The terms “protein,” “peptide,” and “polypeptide” are usedinterchangeably herein, and refer to a polymer of amino acid residueslinked together by peptide (amide) bonds. The terms refer to a protein,peptide, or polypeptide of any size, structure, or function. Typically,a protein, peptide, or polypeptide will be at least three amino acidslong. A protein, peptide, or polypeptide may refer to an individualprotein or a collection of proteins. One or more of the amino acids in aprotein, peptide, or polypeptide may be modified, for example, by theaddition of a chemical entity such as a carbohydrate group, a hydroxylgroup, a phosphate group, a farnesyl group, an isofarnesyl group, afatty acid group, a linker for conjugation, functionalization, or othermodification, etc. A protein, peptide, or polypeptide may also be asingle molecule or may be a multi-molecular complex. A protein, peptide,or polypeptide may be just a fragment of a naturally occurring proteinor peptide. A protein, peptide, or polypeptide may be naturallyoccurring, recombinant, or synthetic, or any combination thereof. Aprotein may comprise different domains, for example, a nucleic acidbinding domain and a nucleic acid cleavage domain. In some embodiments,a protein comprises a proteinaceous part, e.g., an amino acid sequenceconstituting a nucleic acid binding domain, and an organic compound,e.g., a compound that can act as a nucleic acid cleavage agent. In someembodiments, a protein is in a complex with, or is in association with,a nucleic acid, e.g., RNA.

The term “randomized,” as used herein in the context of nucleic acidsequences, refers to a sequence or residue within a sequence that hasbeen synthesized to incorporate a mixture of free nucleotides, forexample, a mixture of all four nucleotides A, T, G, and C. Randomizedresidues are typically represented by the letter N within a nucleotidesequence. In some embodiments, a randomized sequence or residue is fullyrandomized, in which case the randomized residues are synthesized byadding equal amounts of the nucleotides to be incorporated (e.g., 25% T,25% A, 25% G, and 25% C) during the synthesis step of the respectivesequence residue. In some embodiments, a randomized sequence or residueis partially randomized, in which case the randomized residues aresynthesized by adding non-equal amounts of the nucleotides to beincorporated (e.g., 79% T, 7% A, 7% G, and 7% C) during the synthesisstep of the respective sequence residue. Partial randomization allowsfor the generation of sequences that are templated on a given sequence,but have incorporated mutations at a desired frequency. For example, ifa known nuclease target site is used as a synthesis template, partialrandomization in which at each step the nucleotide represented at therespective residue is added to the synthesis at 79%, and the other threenucleotides are added at 7% each, will result in a mixture of partiallyrandomized target sites being synthesized, which still represent theconsensus sequence of the original target site, but which differ fromthe original target site at each residue with a statistical frequency of21% for each residue so synthesized (distributed binomially). In someembodiments, a partially randomized sequence differs from the consensussequence by more than 5%, more than 10%, more than 15%, more than 20%,more than 25%, or more than 30% on average, distributed binomially. Insome embodiments, a partially randomized sequence differs from theconsensus site by no more than 10%, no more than 15%, no more than 20%,no more than 25%, nor more than 30%, no more than 40%, or no more than50% on average, distributed binomially.

The term “RNA-programmable nuclease,” and “RNA-guided nuclease” are usedinterchangeably herein and refer to a nuclease that forms a complex with(e.g., binds or associates with) one or more RNA that is not a targetfor cleavage. In some embodiments, an RNA-programmable nuclease, when ina complex with an RNA, may be referred to as a nuclease:RNA complex.Typically, the bound RNA(s) is referred to as a guide RNA (gRNA) or asingle-guide RNA (sgRNA). The gRNA/sgRNA comprises a nucleotide sequencethat complements a target site, which mediates binding of thenuclease/RNA complex to said target site and providing the sequencespecificity of the nuclease:RNA complex. In some embodiments, theRNA-programmable nuclease is the (CRISPR-associated system) Cas9endonuclease, for example Cas9 (Csn1) from Streptococcus pyogenes (see,e.g., “Complete genome sequence of an M1 strain of Streptococcuspyogenes.” Ferretti J. J., McShan W. M., Ajdic D. J., Savic D. J., SavicG., Lyon K., Primeaux C., Sezate S., Suvorov A. N., Kenton S., Lai H.S., Lin S. P., Qian Y., Jia H. G., Najar F. Z., Ren Q., Zhu H., Song L.expand/collapse author list McLaughlin R. E., Proc. Natl. Acad. Sci.U.S.A. 98:4658-4663(2001); “CRISPR RNA maturation by trans-encoded smallRNA and host factor RNase III.” Deltcheva E., Chylinski K., Sharma C.M., Gonzales K., Chao Y., Pirzada Z. A., Eckert M. R., Vogel J.,Charpentier E., Nature 471:602-607(2011); and “A programmabledual-RNA-guided DNA endonuclease in adaptive bacterial immunity.” JinekM., Chylinski K., Fonfara I., Hauer M., Doudna J. A., Charpentier E.Science 337:816-821(2012), the entire contents of each of which areincorporated herein by reference

Because RNA-programmable nucleases (e.g., Cas9) use RNA:DNAhybridization to determine target DNA cleavage sites, these proteins areable to cleave, in principle, any sequence specified by the guide RNA.Methods of using RNA-programmable nucleases, such as Cas9, forsite-specific cleavage (e.g., to modify a genome) are known in the art(See e.g., Cong, L. et al. Multiplex genome engineering using CRISPR/Cassystems. Science 339, 819-823 (2013); Mali, P. et al. RNA-guided humangenome engineering via Cas9. Science 339, 823-826 (2013); Hwang, W. Y.et al. Efficient genome editing in zebrafish using a CRISPR-Cas system.Nature biotechnology 31, 227-229 (2013); Jinek, M. et al. RNA-programmedgenome editing in human cells. eLife 2, e00471 (2013); Dicarlo, J. E. etal. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cassystems. Nucleic acids research (2013); Jiang, W. et al. RNA-guidedediting of bacterial genomes using CRISPR-Cas systems. Naturebiotechnology 31, 233-239 (2013); the entire contents of each of whichare incorporated herein by reference).

The terms “small molecule” and “organic compound” are usedinterchangeably herein and refer to molecules, whethernaturally-occurring or artificially created (e.g., via chemicalsynthesis) that have a relatively low molecular weight. Typically, anorganic compound contains carbon. An organic compound may containmultiple carbon-carbon bonds, stereocenters, and other functional groups(e.g., amines, hydroxyl, carbonyls, or heterocyclic rings). In someembodiments, organic compounds are monomeric and have a molecular weightof less than about 1500 g/mol. In certain embodiments, the molecularweight of the small molecule is less than about 1000 g/mol or less thanabout 500 g/mol. In certain embodiments, the small molecule is a drug,for example, a drug that has already been deemed safe and effective foruse in humans or animals by the appropriate governmental agency orregulatory body. In certain embodiments, the organic molecule is knownto bind and/or cleave a nucleic acid. In some embodiments, the organiccompound is an enediyne. In some embodiments, the organic compound is anantibiotic drug, for example, an anticancer antibiotic such asdynemicin, neocarzinostatin, calicheamicin, esperamicin, bleomycin, or aderivative thereof.

The term “subject,” as used herein, refers to an individual organism,for example, an individual mammal. In some embodiments, the subject is ahuman. In some embodiments, the subject is a non-human mammal. In someembodiments, the subject is a non-human primate. In some embodiments,the subject is a rodent. In some embodiments, the subject is a sheep, agoat, a cattle, a cat, or a dog. In some embodiments, the subject is avertebrate, an amphibian, a reptile, a fish, an insect, a fly, or anematode.

The terms “target nucleic acid,” and “target genome,” as used herein inthe context of nucleases, refer to a nucleic acid molecule or a genome,respectively, that comprises at least one target site of a givennuclease.

The term “target site,” used herein interchangeably with the term“nuclease target site,” refers to a sequence within a nucleic acidmolecule that is bound and cleaved by a nuclease. A target site may besingle-stranded or double-stranded. In the context of nucleases thatdimerize, for example, nucleases comprising a FokI DNA cleavage domain,a target sites typically comprises a left-half site (bound by onemonomer of the nuclease), a right-half site (bound by the second monomerof the nuclease), and a spacer sequence between the half sites in whichthe cut is made. This structure ([left-half site]-[spacersequence]-[right-half site]) is referred to herein as an LSR structure.In some embodiments, the left-half site and/or the right-half site isbetween 10-18 nucleotides long. In some embodiments, either or bothhalf-sites are shorter or longer. In some embodiments, the left andright half sites comprise different nucleic acid sequences. In thecontext of zinc finger nucleases, target sites may, in some embodimentscomprise two half-sites that are each 6-18 bp long flanking anon-specified spacer region that is 4-8 bp long. In the context ofTALENs, target sites may, in some embodiments, comprise two half-sitessites that are each 10-23 bp long flanking a non-specified spacer regionthat is 10-30 bp long. In the context of RNA-guided (e.g.,RNA-programmable) nucleases, a target site typically comprises anucleotide sequence that is complementary to the sgRNA of theRNA-programmable nuclease, and a protospacer adjacent motif (PAM) at the3′ end adjacent to the sgRNA-complementary sequence. For the RNA-guidednuclease Cas9, the target site may be, in some embodiments, 20 basepairs plus a 3 base pair PAM (e.g., NNN, wherein N represents anynucleotide). Typically, the first nucleotide of a PAM can be anynucleotide, while the two downstream nucleotides are specified dependingon the specific RNA-guided nuclease. Exemplary target sites forRNA-guided nucleases, such as Cas9, are known to those of skill in theart and include, without limitation, NNG, NGN, NAG, and NGG, wherein Nrepresents any nucleotide. In addition, Cas9 nucleases from differentspecies (e.g., S. thermophilus instead of S. pyogenes) recognizes a PAMthat comprises the sequence NGGNG. Additional PAM sequences are known,including, but not limited to NNAGAAW and NAAR (see, e.g., Esvelt andWang, Molecular Systems Biology, 9:641 (2013), the entire contents ofwhich are incorporated herein by reference). For example, the targetsite of an RNA-guided nuclease, such as, e.g., Cas9, may comprise thestructure [N_(Z)]-[PAM], where each N is, independently, any nucleotide,and _(Z) is an integer between 1 and 50. In some embodiments, _(Z) is atleast 2, at least 3, at least 4, at least 5, at least 6, at least 7, atleast 8, at least 9, at least 10, at least 11, at least 12, at least 13,at least 14, at least 15, at least 16, at least 17, at least 18, atleast 19, at least 20, at least 25, at least 30, at least 35, at least40, at least 45, or at least 50. In some embodiments, _(Z) is 5, 6, 7,8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, or 50. In some embodiments, Z is 20.

The term “Transcriptional Activator-Like Effector,” (TALE) as usedherein, refers to bacterial proteins comprising a DNA binding domain,which contains a highly conserved 33-34 amino acid sequence comprising ahighly variable two-amino acid motif (Repeat Variable Diresidue, RVD).The RVD motif determines binding specificity to a nucleic acid sequence,and can be engineered according to methods well known to those of skillin the art to specifically bind a desired DNA sequence (see, e.g.,Miller, Jeffrey; et. al. (February 2011). “A TALE nuclease architecturefor efficient genome editing”. Nature Biotechnology 29 (2): 143-8;Zhang, Feng; et. al. (February 2011). “Efficient construction ofsequence-specific TAL effectors for modulating mammalian transcription”.Nature Biotechnology 29 (2): 149-53; Geiβler, R.; Scholze, H.; Hahn, S.;Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J. (2011), Shiu,Shin-Han. ed. “Transcriptional Activators of Human Genes withProgrammable DNA-Specificity”. PLoS ONE 6 (5): e19509; Boch, Jens(February 2011). “TALEs of genome targeting”. Nature Biotechnology 29(2): 135-6; Boch, Jens; et. al. (December 2009). “Breaking the Code ofDNA Binding Specificity of TAL-Type III Effectors”. Science 326 (5959):1509-12; and Moscou, Matthew J.; Adam J. Bogdanove (December 2009). “ASimple Cipher Governs DNA Recognition by TAL Effectors”. Science 326(5959): 1501; the entire contents of each of which are incorporatedherein by reference). The simple relationship between amino acidsequence and DNA recognition has allowed for the engineering of specificDNA binding domains by selecting a combination of repeat segmentscontaining the appropriate RVDs.

The term “Transcriptional Activator-Like Element Nuclease,” (TALEN) asused herein, refers to an artificial nuclease comprising atranscriptional activator like effector DNA binding domain to a DNAcleavage domain, for example, a FokI domain. A number of modularassembly schemes for generating engineered TALE constructs have beenreported (see e.g., Zhang, Feng; et. al. (February 2011). “Efficientconstruction of sequence-specific TAL effectors for modulating mammaliantranscription”. Nature Biotechnology 29 (2): 149-53; Geiβler, R.;Scholze, H.; Hahn, S.; Streubel, J.; Bonas, U.; Behrens, S. E.; Boch, J.(2011), Shiu, Shin-Han. ed. “Transcriptional Activators of Human Geneswith Programmable DNA-Specificity”. PLoS ONE 6 (5): e19509; Cermak, T.;Doyle, E. L.; Christian, M.; Wang, L.; Zhang, Y.; Schmidt, C.; Baller,J. A.; Somia, N. V. et al. (2011). “Efficient design and assembly ofcustom TALEN and other TAL effector-based constructs for DNA targeting”.Nucleic Acids Research; Morbitzer, R.; Elsaesser, J.; Hausner, J.;Lahaye, T. (2011). “Assembly of custom TALE-type DNA binding domains bymodular cloning”. Nucleic Acids Research; Li, T.; Huang, S.; Zhao, X.;Wright, D. A.; Carpenter, S.; Spalding, M. H.; Weeks, D. P.; Yang, B.(2011). “Modularly assembled designer TAL effector nucleases fortargeted gene knockout and gene replacement in eukaryotes”. NucleicAcids Research.; Weber, E.; Gruetzner, R.; Werner, S.; Engler, C.;Marillonnet, S. (2011). Bendahmane, Mohammed. ed. “Assembly of DesignerTAL Effectors by Golden Gate Cloning”. PLoS ONE 6 (5): e19722; theentire contents of each of which are incorporated herein by reference).

The terms “treatment,” “treat,” and “treating,” refer to a clinicalintervention aimed to reverse, alleviate, delay the onset of, or inhibitthe progress of a disease or disorder, or one or more symptoms thereof,as described herein. As used herein, the terms “treatment,” “treat,” and“treating” refer to a clinical intervention aimed to reverse, alleviate,delay the onset of, or inhibit the progress of a disease or disorder, orone or more symptoms thereof, as described herein. In some embodiments,treatment may be administered after one or more symptoms have developedand/or after a disease has been diagnosed. In other embodiments,treatment may be administered in the absence of symptoms, e.g., toprevent or delay onset of a symptom or inhibit onset or progression of adisease. For example, treatment may be administered to a susceptibleindividual prior to the onset of symptoms (e.g., in light of a historyof symptoms and/or in light of genetic or other susceptibility factors).Treatment may also be continued after symptoms have resolved, forexample to prevent or delay their recurrence.

The term “zinc finger,” as used herein, refers to a small nucleicacid-binding protein structural motif characterized by a fold and thecoordination of one or more zinc ions that stabilize the fold. Zincfingers encompass a wide variety of differing protein structures (see,e.g., Klug A, Rhodes D (1987). “Zinc fingers: a novel protein fold fornucleic acid recognition”. Cold Spring Harb. Symp. Quant. Biol. 52:473-82, the entire contents of which are incorporated herein byreference). Zinc fingers can be designed to bind a specific sequence ofnucleotides, and zinc finger arrays comprising fusions of a series ofzinc fingers, can be designed to bind virtually any desired targetsequence. Such zinc finger arrays can form a binding domain of aprotein, for example, of a nuclease, e.g., if conjugated to a nucleicacid cleavage domain. Different type of zinc finger motifs are known tothose of skill in the art, including, but not limited to, Cys₂His₂, Gagknuckle, Treble clef, Zinc ribbon, Zn₂/Cys₆, and TAZ2 domain-like motifs(see, e.g., Krishna S S, Majumdar I, Grishin N V (January 2003).“Structural classification of zinc fingers: survey and summary”. NucleicAcids Res. 31 (2): 532-50). Typically, a single zinc finger motif binds3 or 4 nucleotides of a nucleic acid molecule. Accordingly, a zincfinger domain comprising 2 zinc finger motifs may bind 6-8 nucleotides,a zinc finger domain comprising 3 zinc finger motifs may bind 9-12nucleotides, a zinc finger domain comprising 4 zinc finger motifs maybind 12-16 nucleotides, and so forth. Any suitable protein engineeringtechnique can be employed to alter the DNA-binding specificity of zincfingers and/or design novel zinc finger fusions to bind virtually anydesired target sequence from 3-30 nucleotides in length (see, e.g., PaboC O, Peisach E, Grant R A (2001). “Design and selection of novelcys2His2 Zinc finger proteins”. Annual Review of Biochemistry 70:313-340; Jamieson A C, Miller J C, Pabo C O (2003). “Drug discovery withengineered zinc-finger proteins”. Nature Reviews Drug Discovery 2 (5):361-368; and Liu Q, Segal D J, Ghiara J B, Barbas C F (May 1997).“Design of polydactyl zinc-finger proteins for unique addressing withincomplex genomes”. Proc. Natl. Acad. Sci. U.S.A. 94 (11); the entirecontents of each of which are incorporated herein by reference). Fusionsbetween engineered zinc finger arrays and protein domains that cleave anucleic acid can be used to generate a “zinc finger nuclease.” A zincfinger nuclease typically comprises a zinc finger domain that binds aspecific target site within a nucleic acid molecule, and a nucleic acidcleavage domain that cuts the nucleic acid molecule within or inproximity to the target site bound by the binding domain. Typicalengineered zinc finger nucleases comprise a binding domain havingbetween 3 and 6 individual zinc finger motifs and binding target sitesranging from 9 base pairs to 18 base pairs in length. Longer targetsites are particularly attractive in situations where it is desired tobind and cleave a target site that is unique in a given genome.

The term “zinc finger nuclease,” as used herein, refers to a nucleasecomprising a nucleic acid cleavage domain conjugated to a binding domainthat comprises a zinc finger array. In some embodiments, the cleavagedomain is the cleavage domain of the type II restriction endonucleaseFokI. Zinc finger nucleases can be designed to target virtually anydesired sequence in a given nucleic acid molecule for cleavage, and thepossibility to the design zinc finger binding domains to bind uniquesites in the context of complex genomes allows for targeted cleavage ofa single genomic site in living cells, for example, to achieve atargeted genomic alteration of therapeutic value. Targeting adouble-strand break to a desired genomic locus can be used to introduceframe-shift mutations into the coding sequence of a gene due to theerror-prone nature of the non-homologous DNA repair pathway. Zinc fingernucleases can be generated to target a site of interest by methods wellknown to those of skill in the art. For example, zinc finger bindingdomains with a desired specificity can be designed by combiningindividual zinc finger motifs of known specificity. The structure of thezinc finger protein Zif268 bound to DNA has informed much of the work inthis field and the concept of obtaining zinc fingers for each of the 64possible base pair triplets and then mixing and matching these modularzinc fingers to design proteins with any desired sequence specificityhas been described (Pavletich N P, Pabo C O (May 1991). “Zinc finger-DNArecognition: crystal structure of a Zif268-DNA complex at 2.1 A”.Science 252 (5007): 809-17, the entire contents of which areincorporated herein). In some embodiments, separate zinc fingers thateach recognize a 3 base pair DNA sequence are combined to generate 3-,4-, 5-, or 6-finger arrays that recognize target sites ranging from 9base pairs to 18 base pairs in length. In some embodiments, longerarrays are contemplated. In other embodiments, 2-finger modulesrecognizing 6-8 nucleotides are combined to generate 4-, 6-, or 8-zincfinger arrays. In some embodiments, bacterial or phage display isemployed to develop a zinc finger domain that recognizes a desirednucleic acid sequence, for example, a desired nuclease target site of3-30 bp in length. Zinc finger nucleases, in some embodiments, comprisea zinc finger binding domain and a cleavage domain fused or otherwiseconjugated to each other via a linker, for example, a polypeptidelinker. The length of the linker determines the distance of the cut fromthe nucleic acid sequence bound by the zinc finger domain. If a shorterlinker is used, the cleavage domain will cut the nucleic acid closer tothe bound nucleic acid sequence, while a longer linker will result in agreater distance between the cut and the bound nucleic acid sequence. Insome embodiments, the cleavage domain of a zinc finger nuclease has todimerize in order to cut a bound nucleic acid. In some such embodiments,the dimer is a heterodimer of two monomers, each of which comprise adifferent zinc finger binding domain. For example, in some embodiments,the dimer may comprise one monomer comprising zinc finger domain Aconjugated to a FokI cleavage domain, and one monomer comprising zincfinger domain B conjugated to a FokI cleavage domain. In thisnonlimiting example, zinc finger domain A binds a nucleic acid sequenceon one side of the target site, zinc finger domain B binds a nucleicacid sequence on the other side of the target site, and the dimerizeFokI domain cuts the nucleic acid in between the zinc finger domainbinding sites.

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS OF THE INVENTIONIntroduction

Site-specific nucleases are powerful tools for targeted genomemodification in vitro or in vivo. Some site specific nucleases cantheoretically achieve a level of specificity for a target cleavage sitethat would allow one to target a single unique site in a genome forcleavage without affecting any other genomic site. It has been reportedthat nuclease cleavage in living cells triggers a DNA repair mechanismthat frequently results in a modification of the cleaved, repairedgenomic sequence, for example, via homologous recombination.Accordingly, the targeted cleavage of a specific unique sequence withina genome opens up new avenues for gene targeting and gene modificationin living cells, including cells that are hard to manipulate withconventional gene targeting methods, such as many human somatic orembryonic stem cells. Nuclease-mediated modification of disease-relatedsequences, e.g., the CCR-5 allele in HIV/AIDS patients, or of genesnecessary for tumor neovascularization, can be used in the clinicalcontext, and two site specific nucleases are currently in clinicaltrials.

One important aspect in the field of site-specific nuclease-mediatedmodification are off-target nuclease effects, e.g., the cleavage ofgenomic sequences that differ from the intended target sequence by oneor more nucleotides. Undesired side effects of off-target cleavage rangefrom insertion into unwanted loci during a gene targeting event tosevere complications in a clinical scenario. Off-target cleavage ofsequences encoding essential gene functions or tumor suppressor genes byan endonuclease administered to a subject may result in disease or evendeath of the subject. Accordingly, it is desirable to characterize thecleavage preferences of a nuclease before using it in the laboratory orthe clinic in order to determine its efficacy and safety. Further, thecharacterization of nuclease cleavage properties allows for theselection of the nuclease best suited for a specific task from a groupof candidate nucleases, or for the selection of evolution productsobtained from a plurality of nucleases. Such a characterization ofnuclease cleavage properties may also inform the de-novo design ofnucleases with enhanced properties, such as enhanced specificity orefficiency.

In many scenarios where a nuclease is employed for the targetedmanipulation of a nucleic acid, cleavage specificity is a crucialfeature. The imperfect specificity of some engineered nuclease bindingdomains can lead to off-target cleavage and undesired effects both invitro and in vivo. Current methods of evaluating site-specific nucleasespecificity, including ELISA assays, microarrays, one-hybrid systems,SELEX, and its variants, and Rosetta-based computational predictions,are all premised on the assumption that the binding specificity of thenuclease is equivalent or proportionate to their cleavage specificity.

It was previously discovered that the prediction of nuclease off-targetbinding effects constitute an imperfect approximation of a nuclease'soff-target cleavage effects that may result in undesired biologicaleffects (see PCT Application WO 2013/066438; and Pattanayak, V.,Ramirez, C. L., Joung, J. K. & Liu, D. R. Revealing off-target cleavagespecificities of zinc-finger nucleases by in vitro selection. Naturemethods 8, 765-770 (2011), the entire contents of each of which areincorporated herein by reference). This finding was consistent with thenotion that the reported toxicity of some site specific DNA nucleasesresults from off-target DNA cleavage, rather than off-target bindingalone.

The methods and reagents of the present disclosure represent, in someaspects, an improvement over previous methods and allow for an accurateevaluation of a given nuclease's target site specificity and providestrategies for the selection of suitable unique target sites and thedesign or selection of highly specific nucleases for the targetedcleavage of a single site in the context of a complex genome. Forexample, some previously reported methods for determining nucleasetarget site specificity profiles by screening libraries of nucleic acidmolecules comprising candidate target sites relied on a “two-cut” invitro selection method which requires indirect reconstruction of targetsites from sequences of two half-sites resulting from two adjacent cutsof the nuclease of a library member nucleic acid (see e.g., Pattanayak,V. et al., Nature Methods 8, 765-770 (2011)). In contrast to such“two-cut” strategies, the methods of the present disclosure utilize a“one cut” screening strategy, which allows for the identification oflibrary members that have been cut at least once by the nuclease. The“one-cut” selection strategies provided herein are compatible withsingle end high-throughput sequencing methods and do not requirecomputational reconstruction of cleaved target sites from cut half-sitesbecause they feature, in some embodiments, direct sequencing of anintact target nuclease sequence in a cut library member nucleic acid.

Additionally, the presently disclosed “one-cut” screening methodsutilize concatemers of a candidate nuclease target site and constantinsert region that are about 10-fold shorter than previously reportedconstructs used for two-cut strategies (˜50 bp repeat sequence lengthversus ˜500 bp repeat sequence length in previous reports). Thisdifference in repeat sequence length in the concatemers of the libraryallows for the generation of highly complex libraries of candidatenuclease target sites, e.g., of libraries comprising 10¹² differentcandidate nuclease target sequences. As described herein, an exemplarylibrary of such complexity has been generated, templated on a known Cas9nuclease target site by varying the sequence of the known target site.The exemplary library demonstrated that a greater than 10-fold coverageof all sequences with eight or fewer mutations of the known target sitecan be achieved using the strategies provided herein. The use of ashorter repeat sequence also allows the use of single-end sequencing,since both a cut half-site and an adjacent uncut site of the samelibrary member are contained within a 100 nucleotide sequencing read.

The strategies, methods, libraries, and reagents provided herein can beutilized to analyze the sequence preferences and specificity of anysite-specific nuclease, for example, to Zinc Finger Nucleases (ZFNs),Transcription Activator-Like Effector Nucleases (TALENs), homingendonucleases, organic compound nucleases, and enediyne antibiotics(e.g., dynemicin, neocarzinostatin, calicheamicin, esperamicin,bleomycin). Suitable nucleases in addition to the ones described hereinwill be apparent to those of skill in the art based on this disclosure.

Further, the methods, reagents, and strategies provided herein allowthose of skill in the art to identify, design, and/or select nucleaseswith enhanced specificity and minimize the off-target effects of anygiven nuclease (e.g., site-specific nucleases such as ZFNs, and TALENSwhich produce cleavage products with sticky ends, as well asRNA-programmable nucleases, for example Cas9, which produce cleavageproducts having blunt ends). While of particular relevance to DNA andDNA-cleaving nucleases, the inventive concepts, methods, strategies, andreagents provided herein are not limited in this respect, but can beapplied to any nucleic acid:nuclease pair.

Identifying Nuclease Target Sites Cleaved by a Site-Specific Nuclease

Some aspects of this disclosure provide improved methods and reagents todetermine the nucleic acid target sites cleaved by any site-specificnuclease. The methods provided herein can be used for the evaluation oftarget site preferences and specificity of both nucleases that createblunt ends and nucleases that create sticky ends. In general, suchmethods comprise contacting a given nuclease with a library of targetsites under conditions suitable for the nuclease to bind and cut atarget site, and determining which target sites the nuclease actuallycuts. A determination of a nuclease's target site profile based onactual cutting has the advantage over methods that rely on binding inthat it measures a parameter more relevant for mediating undesiredoff-target effects of site-specific nucleases. In general, the methodsprovided herein comprise ligating an adapter of a known sequence tonucleic acid molecules that have been cut by a nuclease of interest via5′-phosphate-dependent ligation. Accordingly, the methods providedherein are particularly useful for identifying target sites cut bynucleases that leave a phosphate moiety at the 5′-end of the cut nucleicacid strand when cleaving their target site. After ligating an adapterto the 5′-end of a cut nucleic acid strand, the cut strand can directlybe sequenced using the adapter as a sequencing linker, or a part of thecut library member concatemer comprising an intact target site identicalto the cut target site can be amplified via PCR and the amplificationproduct can then be sequenced.

In some embodiments, the method comprises (a) providing a nuclease thatcuts a double-stranded nucleic acid target site, wherein cutting of thetarget site results in cut nucleic acid strands comprising a5′-phosphate moiety; (b) contacting the nuclease of (a) with a libraryof candidate nucleic acid molecules, wherein each nucleic acid moleculecomprises a concatemer of a sequence comprising a candidate nucleasetarget site and a constant insert sequence, under conditions suitablefor the nuclease to cut a candidate nucleic acid molecule comprising atarget site of the nuclease; and (c) identifying nuclease target sitescut by the nuclease in (b) by determining the sequence of an uncutnuclease target site on the nucleic acid strand that was cut by thenuclease in step (b).

In some embodiments, the method comprises providing a nuclease andcontacting the nuclease with a library of candidate nucleic acidmolecules comprising candidate target sites. In some embodiments, thecandidate nucleic acid molecules are double-stranded nucleic acidmolecules. In some embodiments, the candidate nucleic acid molecules areDNA molecules. In some embodiments, each nucleic acid molecule in thelibrary comprises a concatemer of a sequence comprising a candidatenuclease target site and a constant insert sequence. For example, insome embodiments, the library comprises nucleic acid molecules thatcomprise the structure R₁-[(candidate nuclease target site)-(constantinsert sequence)]_(n)-R₂, wherein R₁ and R₂ are, independently, nucleicacid sequences that may comprise a fragment of the [(candidate nucleasetarget site)-(constant insert sequence)] structure, and n is an integerbetween 2 and y. In some embodiments, y is at least 10¹, at least 10²,at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, atleast 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², atleast 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y isless than 10², less than 10³, less than 10⁴, less than 10⁵, less than10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, lessthan 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than10¹⁵

For example, in some embodiments, the candidate nucleic acid moleculesof the library comprise a candidate nuclease target site of thestructure [(N_(Z))-(PAM)], and, thus, the nucleic acid molecules of thelibrary comprise the structure R₁—[(N_(Z))-(PAM)-(constantregion)]_(X)-R₂, wherein R₁ and R₂ are, independently, nucleic acidsequences that may comprise a fragment of the [(N_(Z))-(PAM)-(constantregion)] repeat unit; each N represents, independently, any nucleotide;Z is an integer between 1 and 50; and X is an integer between 2 and y.In some embodiments, y is at least 10¹, at least 10², at least 10³, atleast 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least 10⁸, atleast 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least 10¹³,at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is less than10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶, lessthan 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than 10¹¹,less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵. Insome embodiments, Z is at least 2, at least 3, at least 4, at least 5,at least 6, at least 7, at least 8, at least 9, at least 10, at least11, at least 12, at least 13, at least 14, at least 15, at least 16, atleast 17, at least 18, at least 19, at least 20, at least 25, at least30, at least 35, at least 40, at least 45, or at least 50. In someembodiments, Z is 20. Each N represents, independently, any nucleotide.Accordingly, a sequence provided as N_(Z) with _(Z)=2 would be NN, witheach N, independently, representing A, T, G, or C. Accordingly, N_(Z)with _(Z)=2 can represent AA, AT, AG, AC, TA, TT, TG, TC, GA, GT, GG,GC, CA, CT, CG, and CC.

In other embodiments, the candidate nucleic acid molecules of thelibrary comprise a candidate nuclease target site of the structure[left-half site]-[spacer sequence]-[right-half site] (“LSR”), and, thus,the nucleic acid molecules of the library comprise the structureR₁-[(LSR)-(constant region)]_(X)-R₂, wherein R₁ and R₂ are,independently, nucleic acid sequences that may comprise a fragment ofthe [(LSR)-(constant region)] repeat unit, and X is an integer between 2and y. In some embodiments, y is at least 10¹, at least 10², at least10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, at least10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², at least10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y is lessthan 10², less than 10³, less than 10⁴, less than 10⁵, less than 10⁶,less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, less than10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than 10¹⁵.The constant region, in some embodiments, is of a length that allows forefficient self-ligation of a single repeat unit. Suitable lengths willbe apparent to those of skill in the art. For example, in someembodiments, the constant region is between 5 and 100 base pairs long,for example, about 5 base pairs, about 10 base pairs, about 15 basepairs, about 20 base pairs, about 25 base pairs, about 30 base pairs,about 35 base pairs, about 40 base pairs, about 50 base pairs, about 60base pairs, about 70 base pairs, about 80 base pairs, about 90 basepairs, or about 100 base pairs long. In some embodiments, the constantregion is 16 base pairs long. In some embodiments, the nuclease cuts adouble-stranded nucleic acid target site and creates blunt ends. Inother embodiments, the nuclease creates a 5′-overhang. In some suchembodiments, the target site comprises a [left-half site]-[spacersequence]-[right-half site] (LSR) structure, and the nuclease cuts thetarget site within the spacer sequence.

In some embodiments, a nuclease cuts a double-stranded target site andcreates blunt ends. In some embodiments, a nuclease cuts adouble-stranded target site and creates an overhang, or sticky end, forexample, a 5′-overhang. In some such embodiments, the method comprisesfilling in the 5′-overhangs of nucleic acid molecules produced from anucleic acid molecule that has been cut once by the nuclease, whereinthe nucleic acid molecules comprise a constant insert sequence flankedby a left or right half-site and cut spacer sequence on one side, and anuncut target site sequence on the other side, thereby creating bluntends.

In some embodiments, the determining of step (c) comprises ligating afirst nucleic acid adapter to the 5′ end of a nucleic acid strand thatwas cut by the nuclease in step (b) via 5′-phosphate-dependent ligation.In some embodiments, the nuclease creates blunt ends. In suchembodiments, an adapter can directly be ligated to the blunt endsresulting from the nuclease cut of the target site by contacting the cutlibrary members with a double-stranded, blunt-ended adapter lacking 5′phosphorylation. In some embodiments, the nuclease creates an overhang(sticky end). In some such embodiments, an adapter may be ligated to thecut site by contacting the cut library member with an excess of adapterhaving a compatible sticky end. If a nuclease is used that cuts within aconstant spacer sequence between variable half-sites, the sticky end canbe designed to match the 5′ overhang created from the spacer sequence.In embodiments, where the nuclease cuts within a variable sequence, apopulation of adapters having a variable overhang sequence and aconstant annealed sequence (for use as a sequencing linker or PCRprimer) may be used, or the 5′ overhangs may be filled in to form bluntends before adapter ligation.

In some embodiments, the determining of step (c) further comprisesamplifying a fragment of the concatemer cut by the nuclease thatcomprises an uncut target site via PCR using a PCR primer thathybridizes with the adapter and a PCR primer that hybridizes with theconstant insert sequence. Typically, the amplification of concatemersvia PCR will yield amplicons comprising at least one intact candidatetarget site identical to the cut target sites because the target sitesin each concatemer are identical. For single-direction sequencing, anenrichment of amplicons that comprise one intact target site, no morethan two intact target sites, no more than three intact target sites, nomore than four intact target sites, or no more than five intact targetsites may be desirable. In embodiments where PCR is used foramplification of cut nucleic acid molecules, the PCR parameters can beoptimized to favor the amplification of short sequences and disfavor theamplification of longer sequences, e.g., by using a short elongationtime in the PCR cycle. Another possibility for enrichment of shortamplicons is size fractionation, e.g., via gel electrophoresis or sizeexclusion chromatography. Size fractionation can be performed beforeand/or after amplification. Other suitable methods for enrichment ofshort amplicons will be apparent to those of skill in the art and thedisclosure is not limited in this respect.

In some embodiments, the determining of step (c) comprises sequencingthe nucleic acid strand that was cut by the nuclease in step (b), or acopy thereof obtained via amplification, e.g., by PCR. Sequencingmethods are well known to those of skill in the art. The disclosure isnot limited in this respect.

In some embodiments, the nuclease being profiled using the inventivesystem is an RNA-programmable nuclease that forms a complex with an RNAmolecule, and wherein the nuclease:RNA complex specifically binds anucleic acid sequence complementary to the sequence of the RNA molecule.In some embodiments, the RNA molecule is a single-guide RNA (sgRNA). Insome embodiments, the sgRNA comprises 5-50 nucleotides, 10-30nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides,e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, or 30 nucleotides. In some embodiments, the sgRNAcomprises 5-50 nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22nucleotides, 19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides thatare complementary to a sequence of the nuclease target site. In someembodiments, the sgRNA comprises 20 nucleotides that are complementaryto the nuclease target site. In some embodiments, the nuclease is a Cas9nuclease. In some embodiments, the nuclease target site comprises a[sgRNA-complementary sequence]-[protospacer adjacent motif (PAM)]structure, and the nuclease cuts the target site within thesgRNA-complementary sequence. In some embodiments, thesgRNA-complementary sequence comprises 5-50 nucleotides, 10-30nucleotides, 15-25 nucleotides, 18-22 nucleotides, 19-21 nucleotides,e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, or 30 nucleotides.

In some embodiments, the RNA-programmable nuclease is a Cas9 nuclease.The RNA-programmable Cas9 endonuclease cleaves double-stranded DNA(dsDNA) at sites adjacent to a two-base-pair PAM motif and complementaryto a guide RNA sequence (sgRNA). Typically, the sgRNA sequence that iscomplementary to the target site sequence is about 20 nucleotides long,but shorter and longer complementary sgRNA sequences can be used aswell. For example, in some embodiments, the sgRNA comprises 5-50nucleotides, 10-30 nucleotides, 15-25 nucleotides, 18-22 nucleotides,19-21 nucleotides, e.g., 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21,22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. The Cas9 system hasbeen used to modify genomes in multiple cell types, demonstrating itspotential as a facile genome-engineering tool.

In some embodiments, the nuclease comprises an unspecific nucleic acidcleavage domain. In some embodiments, the nuclease comprises a FokIcleavage domain. In some embodiments, the nuclease comprises a nucleicacid cleavage domain that cleaves a target sequence upon cleavage domaindimerization. In some embodiments, the nuclease comprises a bindingdomain that specifically binds a nucleic acid sequence. In someembodiments, the binding domain comprises a zinc finger. In someembodiments, the binding domain comprises at least 2, at least 3, atleast 4, or at least 5 zinc fingers. In some embodiments, the nucleaseis a Zinc Finger Nuclease. In some embodiments, the binding domaincomprises a Transcriptional Activator-Like Element. In some embodiments,the nuclease is a Transcriptional Activator-Like Element Nuclease(TALEN). In some embodiments, the nuclease is a homing endonuclease. Insome embodiments, the nuclease is an organic compound. In someembodiments, the nuclease comprises an enediyne functional group. Insome embodiments, the nuclease is an antibiotic. In some embodiments,the compound is dynemicin, neocarzinostatin, calicheamicin, esperamicin,bleomycin, or a derivative thereof.

Incubation of the nuclease with the library nucleic acids will result incleavage of those concatemers in the library that comprise target sitesthat can be bound and cleaved by the nuclease. If a given nucleasecleaves a specific target site with high efficiency, a concatemercomprising target sites will be cut, e.g., once or multiple times,resulting in the generation of fragments comprising a cut target siteadjacent to one or more repeat units. Depending on the structure of thelibrary members, an exemplary cut nucleic acid molecule released from alibrary member concatemer by a single nuclease cleavage may, forexample, be of the structure (cut target site)-(constantregion)-[(target site)-(constant region)]_(X)-R₂. For example, in thecontext of an RNA-guided nuclease, an exemplary cut nucleic acidmolecule released from a library member concatemer by a single nucleasecleavage may, for example, be of the structure (PAM)-(constantregion)-[(N_(Z))-(PAM)-(constant region)]_(X)-R₂. And in the context ofa nuclease cutting an LSR structure within the spacer region, anexemplary cut nucleic acid molecule released from a library memberconcatemer by a single nuclease cleavage may, for example, be of thestructure (cut spacer region)-(right half site)-(constantregion)-[(LSR)-(constant region)]_(X)-R₂. Such cut fragments releasedfrom library candidate molecules can then be isolated and/or thesequence of the target site cleaved by the nuclease identified bysequencing an intact target site (e.g., an intact (N_(Z))-(PAM) site ofreleased repeat units. See, e.g., FIG. 1B for an illustration.

Suitable conditions for exposure of the library of nucleic acidmolecules will be apparent to those of skill in the art. In someembodiments, suitable conditions do not result in denaturation of thelibrary nucleic acids or the nuclease and allow for the nuclease toexhibit at least 50%, at least 60%, at least 70%, at least 80%, at least90%, at least 95%, or at least 98% of its nuclease activity.

Additionally, if a given nuclease cleaves a specific target site, somecleavage products will comprise a cut half site and an intact, or uncuttarget site. As described herein, such products can be isolated byroutine methods, and because the insert sequence, in some aspects, isless than 100 base pairs, such isolated cleavage products may besequenced in a single read-through, allowing identification of thetarget site sequence without reconstructing the sequence, e.g., from cuthalf sites.

Any method suitable for isolation and sequencing of the repeat units canbe employed to elucidate the LSR sequence cleaved by the nuclease. Forexample, since the length of the constant region is known, individualreleased repeat units can be separated based on their size from thelarger uncut library nucleic acid molecules as well as from fragments oflibrary nucleic acid molecules that comprise multiple repeat units(indicating non-efficient targeted cleavage by the nuclease). Suitablemethods for separating and/or isolating nucleic acid molecules based ontheir size are well-known to those of skill in the art and include, forexample, size fractionation methods, such as gel electrophoresis,density gradient centrifugation, and dialysis over a semi-permeablemembrane with a suitable molecular cutoff value. The separated/isolatednucleic acid molecules can then be further characterized, for example,by ligating PCR and/or sequencing adapters to the cut ends andamplifying and/or sequencing the respective nucleic acids. Further, ifthe length of the constant region is selected to favor self-ligation ofindividual released repeat units, such individual released repeat unitsmay be enriched by contacting the nuclease treated library moleculeswith a ligase and subsequent amplification and/or sequencing based onthe circularized nature of the self-ligated individual repeat units.

In some embodiments, where a nuclease is used that generates5′-overhangs as a result of cutting a target nucleic acid, the5′-overhangs of the cut nucleic acid molecules are filled in. Methodsfor filling in 5′-overhangs are well known to those of skill in the artand include, for example, methods using DNA polymerase I Klenow fragmentlacking exonuclease activity (Klenow (3′->5′ exo-)). Filling in5′-overhangs results in the overhang-templated extension of the recessedstrand, which, in turn, results in blunt ends. In the case of singlerepeat units released from library concatemers, the resulting structureis a blunt-ended S₂′R-(constant region)-LS₁′, with S₁′ and S₂′comprising blunt ends. PCR and/or sequencing adapters can then be addedto the ends by blunt end ligation and the respective repeat units(including S₂′R and LS₁′ regions) can be sequenced. From the sequencedata, the original LSR region can be deduced. Blunting of the overhangscreated during the nuclease cleavage process also allows fordistinguishing between target sites that were properly cut by therespective nuclease and target sites that were non-specifically cut,e.g., based on non-nuclease effects such as physical shearing. Correctlycleaved nuclease target sites can be recognized by the existence ofcomplementary S₂′R and LS₁′ regions, which comprise a duplication of theoverhang nucleotides as a result of the overhang fill in while targetsites that were not cleaved by the respective nuclease are unlikely tocomprise overhang nucleotide duplications. In some embodiments, themethod comprises identifying the nuclease target site cut by thenuclease by determining the sequence of the left-half site, theright-half-site, and/or the spacer sequence of a released individualrepeat unit. Any suitable method for amplifying and/or sequencing can beused to identify the LSR sequence of the target site cleaved by therespective nuclease. Methods for amplifying and/or sequencing nucleicacids are well known to those of skill in the art and the disclosure isnot limited in this respect. In the case of nucleic acids released fromlibrary concatemers that comprise a cut half site and an uncut targetsite (e.g., comprises at least about 1.5 repeat sequences), filling inthe 5′-overhangs also provides for assurance that the nucleic acid wascleaved by the nuclease. Because the nucleic acid also comprises anintact, or uncut target site, the sequence of said site can bedetermined without having to reconstruct the sequence from a left-halfsite, right-half site, and/or spacer sequence.

Some of the methods and strategies provided herein allow for thesimultaneous assessment of a plurality of candidate target sites aspossible cleavage targets for any given nuclease. Accordingly, the dataobtained from such methods can be used to compile a list of target sitescleaved by a given nuclease, which is also referred to herein as atarget site profile. If a sequencing method is used that allows for thegeneration of quantitative sequencing data, it is also possible torecord the relative abundance of any nuclease target site detected to becleaved by the respective nuclease. Target sites that are cleaved moreefficiently by the nuclease will be detected more frequently in thesequencing step, while target sites that are not cleaved efficientlywill only rarely release an individual repeat unit from a candidateconcatemer, and thus, will only generate few, if any, sequencing reads.Such quantitative sequencing data can be integrated into a target siteprofile to generate a ranked list of highly preferred and less preferrednuclease target sites.

The methods and strategies of nuclease target site profiling providedherein can be applied to any site-specific nuclease, including, forexample, ZFNs, TALENs, homing endonucleases, and RNA-programmablenucleases, such as Cas9 nucleases. As described in more detail herein,nuclease specificity typically decreases with increasing nucleaseconcentration, and the methods described herein can be used to determinea concentration at which a given nuclease efficiently cuts its intendedtarget site, but does not efficiently cut any off-target sequences. Insome embodiments, a maximum concentration of a therapeutic nuclease isdetermined at which the therapeutic nuclease cuts its intended nucleasetarget site but does not cut more than 10, more than 5, more than 4,more than 3, more than 2, more than 1, or any additional sites. In someembodiments, a therapeutic nuclease is administered to a subject in anamount effective to generate a final concentration equal or lower thanthe maximum concentration determined as described above.

In some embodiments, the library of candidate nucleic acid moleculesused in the methods provided herein comprises at least 10⁸, at least10⁹, at least 10¹⁰, at least 10¹¹, or at least 10¹² different candidatenuclease target sites.

In some embodiments, the nuclease is a therapeutic nuclease which cuts aspecific nuclease target site in a gene associated with a disease. Insome embodiments, the method further comprises determining a maximumconcentration of the therapeutic nuclease at which the therapeuticnuclease cuts the specific nuclease target site and does not cut morethan 10, more than 5, more than 4, more than 3, more than 2, more than1, or no additional sites. In some embodiments, the method furthercomprises administering the therapeutic nuclease to a subject in anamount effective to generate a final concentration equal or lower thanthe maximum concentration.

Nuclease Target Site Libraries

Some embodiments of this disclosure provide libraries of nucleic acidmolecules for nuclease target site profiling. In some embodiments, thecandidate nucleic acid molecules of the library comprise the structureR₁—[(N_(Z))-(PAM)-(constant region)]_(X)-R₂, wherein R₁ and R₂ are,independently, nucleic acid sequences that may comprise a fragment ofthe [(N_(Z))-(PAM)-(constant region)] repeat unit; each N represents,independently, any nucleotide; Z is an integer between 1 and 50; and Xis an integer between 2 and y. In some embodiments, y is at least 10¹,at least 10², at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, atleast 10⁷, at least 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, atleast 10¹², at least 10¹³, at least 10¹⁴, or at least 10¹⁵. In someembodiments, y is less than 10², less than 10³, less than 10⁴, less than10⁵, less than 10⁶, less than 10⁷, less than 10⁸, less than 10⁹, lessthan 10¹⁰, less than 10¹¹, less than 10¹², less than 10¹³, less than10¹⁴, or less than 10¹⁵. In some embodiments, Z is at least 2, at least3, at least 4, at least 5, at least 6, at least 7, at least 8, at least9, at least 10, at least 11, at least 12, at least 13, at least 14, atleast 15, at least 16, at least 17, at least 18, at least 19, at least20, at least 25, at least 30, at least 35, at least 40, at least 45, orat least 50. In some embodiments, Z is 20. Each N represents,independently, any nucleotide. Accordingly, a sequence provided as N_(Z)with _(Z)=2 would be NN, with each N, independently, representing A, T,G, or C. Accordingly, N_(Z) with _(Z)=2 can represent AA, AT, AG, AC,TA, TT, TG, TC, GA, GT, GG, GC, CA, CT, CG, and CC.

In some embodiments, a library is provided comprising candidate nucleicacid molecules that comprise target sites with a partially randomizedleft-half site, a partially randomized right-half site, and/or apartially randomized spacer sequence. In some embodiments, the libraryis provided comprising candidate nucleic acid molecules that comprisetarget sites with a partially randomized left half site, a fullyrandomized spacer sequence, and a partially randomized right half site.In some embodiments, a library is provided comprising candidate nucleicacid molecules that comprise target sites with a partially or fullyrandomized sequence, wherein the target sites comprise the structure[N_(Z)-(PAM)], for example as described herein. In some embodiments,partially randomized sites differ from the consensus site by more than5%, more than 10%, more than 15%, more than 20%, more than 25%, or morethan 30% on average, distributed binomially.

In some embodiments such a library comprises a plurality of nucleic acidmolecules, each comprising a concatemer of a candidate nuclease targetsite and a constant insert sequence, also referred to herein as aconstant region. For example, in some embodiments, the candidate nucleicacid molecules of the library comprise the structureR₁-[(sgRNA-complementary sequence)-(PAM)-(constant region)]_(X)-R₂, orthe structure R₁-[(LSR)-(constant region)]_(X)-R₂, wherein the structurein square brackets (“[ . . . ]”) is referred to as a repeat unit orrepeat sequence; R₁ and R₂ are, independently, nucleic acid sequencesthat may comprise a fragment of the repeat unit, and X is an integerbetween 2 and y. In some embodiments, y is at least 10¹, at least 10²,at least 10³, at least 10⁴, at least 10⁵, at least 10⁶, at least 10⁷, atleast 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², atleast 10¹³, at least 10¹⁴, or at least 10¹⁵. In some embodiments, y isless than 10², less than 10³, less than 10⁴, less than 10⁵, less than10⁶, less than 10⁷, less than 10⁸, less than 10⁹, less than 10¹⁰, lessthan 10¹¹, less than 10¹², less than 10¹³, less than 10¹⁴, or less than10¹⁵. The constant region, in some embodiments, is of a length thatallows for efficient self-ligation of a single repeat unit. In someembodiments, the constant region is of a length that allows forefficient separation of single repeat units from fragments comprisingtwo or more repeat units. In some embodiments, the constant region is ofa length allows for efficient sequencing of a complete repeat unit inone sequencing read. Suitable lengths will be apparent to those of skillin the art. For example, in some embodiments, the constant region isbetween 5 and 100 base pairs long, for example, about 5 base pairs,about 10 base pairs, about 15 base pairs, about 20 base pairs, about 25base pairs, about 30 base pairs, about 35 base pairs, about 40 basepairs, about 50 base pairs, about 60 base pairs, about 70 base pairs,about 80 base pairs, about 90 base pairs, or about 100 base pairs long.In some embodiments, the constant region is 1, 2, 3, 4, 5, 6, 7, 8, 9,0, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28,29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46,47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64,65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, or 80 basepairs long.

An LSR site typically comprises a [left-half site]-[spacersequence]-[right-half site] structure. The lengths of the half-size andthe spacer sequence will depend on the specific nuclease to beevaluated. In general, the half-sites will be 6-30 nucleotides long, andpreferably 10-18 nucleotides long. For example, each half siteindividually may be 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19,20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides long. In someembodiments, an LSR site may be longer than 30 nucleotides. In someembodiments, the left half site and the right half site of an LSR are ofthe same length. In some embodiments, the left half site and the righthalf site of an LSR are of different lengths. In some embodiments, theleft half site and the right half site of an LSR are of differentsequences. In some embodiments, a library is provided that comprisescandidate nucleic acids which comprise LSRs that can be cleaved by aFokI cleavage domain, a Zinc Finger Nuclease (ZFN), a TranscriptionActivator-Like Effector Nuclease (TALEN), a homing endonuclease, or anorganic compound (e.g., an enediyne antibiotic such as dynemicin,neocarzinostatin, calicheamicin, and esperamicinl; and bleomycin).

In some embodiments, a library of candidate nucleic acid molecules isprovided that comprises at least 10⁵, at least 10⁶, at least 10⁷, atleast 10⁸, at least 10⁹, at least 10¹⁰, at least 10¹¹, at least 10¹², atleast 10¹³, at least 10¹⁴, or at least 10¹⁵ different candidate nucleasetarget sites. In some embodiments, the candidate nucleic acid moleculesof the library are concatemers produced from a secularized templates byrolling cycle amplification. In some embodiments, the library comprisesnucleic acid molecules, e.g., concatemers, of a molecular weight of atleast 5 kDa, at least 6 kDa, at least 7 kDa, at least 8 kDa, at least 9kDa, at least 10 kDa, at least 12 kDa, or at least 15 kDa. In someembodiments, the molecular weight of the nucleic acid molecules withinthe library may be larger than 15 kDa. In some embodiments, the librarycomprises nucleic acid molecules within a specific size range, forexample, within a range of 5-7 kDa, 5-10 kDa, 8-12 kDa, 10-15 kDa, or12-15 kDa, or 5-10 kDa or any possible subrange. While some methodssuitable for generating nucleic acid concatemers according to someaspects of this disclosure result in the generation of nucleic acidmolecules of greatly different molecular weights, such mixtures ofnucleic acid molecules may be size fractionated to obtain a desired sizedistribution. Suitable methods for enriching nucleic acid molecules of adesired size or excluding nucleic acid molecules of a desired size arewell known to those of skill in the art and the disclosure is notlimited in this respect.

In some embodiments, partially randomized sites differ from theconsensus site by no more than 10%, no more than 15%, no more than 20%,no more than 25%, nor more than 30%, no more than 40%, or no more than50% on average, distributed binomially. For example, in some embodimentspartially randomized sites differ from the consensus site by more than5%, but by no more than 10%; by more than 10%, but by no more than 20%;by more than 20%, but by no more than 25%; by more than 5%, but by nomore than 20%, and so on. Using partially randomized nuclease targetsites in the library is useful to increase the concentration of librarymembers comprising target sites that are closely related to theconsensus site, for example, that differ from the consensus sites inonly one, only two, only three, only four, or only five residues. Therationale behind this is that a given nuclease, for example a given ZFNor RNA-programmable nuclease, is likely to cut its intended target siteand any closely related target sites, but unlikely to cut a target sitesthat is vastly different from or completely unrelated to the intendedtarget site. Accordingly, using a library comprising partiallyrandomized target sites can be more efficient than using librariescomprising fully randomized target sites without compromising thesensitivity in detecting any off-target cleavage events for any givennuclease. Thus, the use of partially randomized libraries significantlyreduces the cost and effort required to produce a library having a highlikelihood of covering virtually all off-target sites of a givennuclease. In some embodiments however it may be desirable to use a fullyrandomized library of target sites, for example, in embodiments, wherethe specificity of a given nuclease is to be evaluated in the context ofany possible site in a given genome.

Selection and Design of Site-Specific Nucleases

Some aspects of this disclosure provide methods and strategies forselecting and designing site-specific nucleases that allow the targetedcleavage of a single, unique sites in the context of a complex genome.In some embodiments, a method is provided that comprises providing aplurality of candidate nucleases that are designed or known to cut thesame consensus sequence; profiling the target sites actually cleaved byeach candidate nuclease, thus detecting any cleaved off-target sites(target sites that differ from the consensus target site); and selectinga candidate nuclease based on the off-target site(s) so identified. Insome embodiments, this method is used to select the most specificnuclease from a group of candidate nucleases, for example, the nucleasethat cleaves the consensus target site with the highest specificity, thenuclease that cleaves the lowest number of off-target sites, thenuclease that cleaves the lowest number of off-target sites in thecontext of a target genome, or a nuclease that does not cleave anytarget site other than the consensus target site. In some embodiments,this method is used to select a nuclease that does not cleave anyoff-target site in the context of the genome of a subject atconcentration that is equal to or higher than a therapeuticallyeffective concentration of the nuclease.

The methods and reagents provided herein can be used, for example, toevaluate a plurality of different nucleases targeting the same intendedtargets site, for example, a plurality of variations of a givensite-specific nuclease, for example a given zinc finger nuclease.Accordingly, such methods may be used as the selection step in evolvingor designing a novel site-specific nucleases with improved specificity.

Identifying Unique Nuclease Target Sites within a Genome

Some embodiments of this disclosure provide a method for selecting anuclease target site within a genome. As described in more detailelsewhere herein, it was surprisingly discovered that off target sitescleaved by a given nuclease are typically highly similar to theconsensus target site, e.g., differing from the consensus target site inonly one, only two, only three, only four, or only five nucleotideresidues. Based on this discovery, a nuclease target sites within thegenome can be selected to increase the likelihood of a nucleasetargeting this site not cleaving any off target sites within the genome.For example, in some embodiments, a method is provided that comprisesidentifying a candidate nuclease target site; and comparing thecandidate nuclease target site to other sequences within the genome.Methods for comparing candidate nuclease target sites to other sequenceswithin the genome are well known to those of skill in the art andinclude for example sequence alignment methods, for example, using asequence alignment software or algorithm such as BLAST on a generalpurpose computer. A suitable unique nuclease target site can then beselected based on the results of the sequence comparison. In someembodiments, if the candidate nuclease target site differs from anyother sequence within the genome by at least 3, at least 4, at least 5,at least 6, at least 7, at least 8, at least 9, or at least 10nucleotides, the nuclease target site is selected as a unique sitewithin the genome, whereas if the site does not fulfill this criteria,the site may be discarded. In some embodiments, once a site is selectedbased on the sequence comparison, as outlined above, a site-specificnuclease targeting the selected site is designed. For example, a zincfinger nuclease may be designed to target any selected nuclease targetsite by constructing a zinc finger array binding the target site, andconjugating the zinc finger array to a DNA cleavage domain. Inembodiments where the DNA cleavage domain needs to dimerize in order tocleave DNA, to zinc finger arrays will be designed, each binding a halfsite of the nuclease target site, and each conjugated to a cleavagedomain. In some embodiments, nuclease designing and/or generating isdone by recombinant technology. Suitable recombinant technologies arewell known to those of skill in the art, and the disclosure is notlimited in this respect.

In some embodiments, a site-specific nuclease designed or generatedaccording to aspects of this disclosure is isolated and/or purified. Themethods and strategies for designing site-specific nucleases accordingto aspects of this disclosure can be applied to design or generate anysite-specific nuclease, including, but not limited to Zinc FingerNucleases, Transcription Activator-Like Effector Nucleases (TALENs), ahoming endonuclease, an organic compound nuclease, or an enediyneantibiotic (e.g., dynemicin, neocarzinostatin, calicheamicin,esperamicin, bleomycin).

Isolated Nucleases

Some aspects of this disclosure provide isolated site-specific nucleaseswith enhanced specificity that are designed using the methods andstrategies described herein. Some embodiments, of this disclosureprovide nucleic acids encoding such nucleases. Some embodiments of thisdisclosure provide expression constructs comprising such encodingnucleic acids. For example, in some embodiments an isolated nuclease isprovided that has been engineered to cleave a desired target site withina genome, and has been evaluated according to a method provided hereinto cut less than 1, less than 2, less than 3, less than 4, less than 5,less than 6, less than 7, less than 8, less than 9 or less than 10off-target sites at a concentration effective for the nuclease to cutits intended target site. In some embodiments an isolated nuclease isprovided that has been engineered to cleave a desired unique target sitethat has been selected to differ from any other site within a genome byat least 3, at least 4, at least 5, at least 6, at least 7, at least 8,at least 9, or at least 10 nucleotide residues. In some embodiments, theisolated nuclease is an RNA-programmable nuclease, such as a Cas9nuclease; a Zinc Finger Nuclease (ZFN); or a TranscriptionActivator-Like Effector Nuclease (TALEN), a homing endonuclease, anorganic compound nuclease, or an enediyne antibiotic (e.g., dynemicin,neocarzinostatin, calicheamicin, esperamicin, bleomycin). In someembodiments, the isolated nuclease cleaves a target site within anallele that is associated with a disease or disorder. In someembodiments, the isolated nuclease cleaves a target site the cleavage ofwhich results in treatment or prevention of a disease or disorder. Insome embodiments, the disease is HIV/AIDS, or a proliferative disease.In some embodiments, the allele is a CCR5 (for treating HIV/AIDS) or aVEGFA allele (for treating a proliferative disease).

In some embodiments, the isolated nuclease is provided as part of apharmaceutical composition. For example, some embodiments providepharmaceutical compositions comprising a nuclease as provided herein, ora nucleic acid encoding such a nuclease, and a pharmaceuticallyacceptable excipient. Pharmaceutical compositions may optionallycomprise one or more additional therapeutically active substances.

In some embodiments, compositions provided herein are administered to asubject, for example, to a human subject, in order to effect a targetedgenomic modification within the subject. In some embodiments, cells areobtained from the subject and contacted with a nuclease or anuclease-encoding nucleic acid ex vivo, and re-administered to thesubject after the desired genomic modification has been effected ordetected in the cells. Although the descriptions of pharmaceuticalcompositions provided herein are principally directed to pharmaceuticalcompositions which are suitable for administration to humans, it will beunderstood by the skilled artisan that such compositions are generallysuitable for administration to animals of all sorts. Modification ofpharmaceutical compositions suitable for administration to humans inorder to render the compositions suitable for administration to variousanimals is well understood, and the ordinarily skilled veterinarypharmacologist can design and/or perform such modification with merelyordinary, if any, experimentation. Subjects to which administration ofthe pharmaceutical compositions is contemplated include, but are notlimited to, humans and/or other primates; mammals, includingcommercially relevant mammals such as cattle, pigs, horses, sheep, cats,dogs, mice, and/or rats; and/or birds, including commercially relevantbirds such as chickens, ducks, geese, and/or turkeys.

Formulations of the pharmaceutical compositions described herein may beprepared by any method known or hereafter developed in the art ofpharmacology. In general, such preparatory methods include the step ofbringing the active ingredient into association with an excipient and/orone or more other accessory ingredients, and then, if necessary and/ordesirable, shaping and/or packaging the product into a desired single-or multi-dose unit.

Pharmaceutical formulations may additionally comprise a pharmaceuticallyacceptable excipient, which, as used herein, includes any and allsolvents, dispersion media, diluents, or other liquid vehicles,dispersion or suspension aids, surface active agents, isotonic agents,thickening or emulsifying agents, preservatives, solid binders,lubricants and the like, as suited to the particular dosage formdesired. Remington's The Science and Practice of Pharmacy, 21^(st)Edition, A. R. Gennaro (Lippincott, Williams & Wilkins, Baltimore, Md.,2006; incorporated in its entirety herein by reference) disclosesvarious excipients used in formulating pharmaceutical compositions andknown techniques for the preparation thereof. See also PCT applicationPCT/US2010/055131, incorporated in its entirety herein by reference, foradditional suitable methods, reagents, excipients and solvents forproducing pharmaceutical compositions comprising a nuclease. Exceptinsofar as any conventional excipient medium is incompatible with asubstance or its derivatives, such as by producing any undesirablebiological effect or otherwise interacting in a deleterious manner withany other component(s) of the pharmaceutical composition, its use iscontemplated to be within the scope of this disclosure.

The function and advantage of these and other embodiments of the presentinvention will be more fully understood from the Examples below. Thefollowing Examples are intended to illustrate the benefits of thepresent invention and to describe particular embodiments, but are notintended to exemplify the full scope of the invention. Accordingly, itwill be understood that the Examples are not meant to limit the scope ofthe invention.

Examples Materials and Methods

Oligonucleotides.

All oligonucleotides used in this study were purchased from IntegratedDNA Technologies. Oligonucleotide sequences are listed in Table 9.

Expression and Purification of S. pyogenes Cas9.

E. coli Rosetta (DE3) cells were transformed with plasmid pMJ806¹¹,encoding the S. pyogenes cas9 gene fused to an N-terminal 6×His-tag/maltose binding protein. The resulting expression strain wasinoculated in Luria-Bertani (LB) broth containing 100 μg/mL ofampicillin and 30 μg/mL of chloramphenicol at 37° C. overnight. Thecells were diluted 1:100 into the same growth medium and grown at 37° C.to OD₆₀₀˜0.6. The culture was incubated at 18° C. for 30 min, andisopropyl β-D-1-thiogalactopyranoside (IPTG) was added at 0.2 mM toinduce Cas9 expression. After −17 h, the cells were collected bycentrifugation at 8,000 g and resuspended in lysis buffer (20 mMtris(hydroxymethyl)-aminomethane (Tris)-HCl, pH 8.0, 1 M KCl, 20%glycerol, 1 mM tris(2-carboxyethyl)phosphine (TCEP)). The cells werelysed by sonication (10 sec pulse-on and 30 sec pulse-off for 10 mintotal at 6 W output) and the soluble lysate was obtained bycentrifugation at 20,000 g for 30 min. The cell lysate was incubatedwith nickel-nitriloacetic acid (nickel-NTA) resin (Qiagen) at 4° C. for20 min to capture His-tagged Cas9. The resin was transferred to a 20-mLcolumn and washed with 20 column volumes of lysis buffer. Cas9 waseluted in 20 mM Tris-HCl (pH 8), 0.1 M KCl, 20% glycerol, 1 mM TCEP, and250 mM imidazole, and concentrated by Amicon ultra centrifugal filter(Millipore, 30-kDa molecular weight cut-off) to −50 mg/mL. The 6× Histag and maltose-binding protein were removed by TEV protease treatmentat 4° C. for 20 h and captured by a second Ni-affinity purificationstep. The eluent, containing Cas9, was injected into a HiTrap SP FFcolumn (GE Healthcare) in purification buffer containing 20 mM Tris-HCl(pH 8), 0.1 M KCl, 20% glycerol, and 1 mM TCEP. Cas9 was eluted withpurification buffer containing a linear KCl gradient from 0.1 M to 1 Mover five column volumes. The eluted Cas9 was further purified by aHiLoad Superdex 200 column in purification buffer, snap-frozen in liquidnitrogen, and stored in aliquots at −80° C.

In Vitro RNA Transcription.

100 pmol CLTA(#) v2.1 fwd and v2.1 template rev were incubated at 95° C.and cooled at 0.1° C./s to 37° C. in NEBuffer2 (50 mM sodium chloride,10 mM Tris-HCl, 10 mM magnesium chloride, 1 mM dithiothreitol, pH 7.9)supplemented with 10 μM dNTP mix (Bio-Rad). 10 U of Klenow Fragment(3′→5′ exo⁻) (NEB) were added to the reaction mixture and adouble-stranded CLTA(#) v2.1 template was obtained by overlap extensionfor 1 h at 37° C. 200 nM CLTA(#) v2.1 template alone or 100 nM CLTA(#)template with 100 nM T7 promoter oligo was incubated overnight at 37° C.with 0.16 U/μL of T7 RNA Polymerase (NEB) in NEB RNAPol Buffer (40 mMTris-HCl, pH 7.9, 6 mM magnesium chloride, 10 mM dithiothreitol, 2 mMspermidine) supplemented with 1 mM rNTP mix (1 mM rATP, 1 mM rCTP, 1 mMrGTP, 1 mM rUTP). In vitro transcribed RNA was precipitated with ethanoland purified by gel electrophoresis on a Criterion 10% polyacrylamideTBE-Urea gel (Bio-Rad). Gel-purified sgRNA was precipitated with ethanoland redissolved in water.

In Vitro Library Construction.

10 pmol of CLTA(#) lib oligonucleotides were separately circularized byincubation with 100 units of CircLigase II ssDNA Ligase (Epicentre) in1× CircLigase II Reaction Buffer (33 mM Tris-acetate, 66 mM potassiumacetate, 0.5 mM dithiothreitol, pH 7.5) supplemented with 2.5 mMmanganese chloride in a total reaction volume of 20 μL for 16 hours at60° C. The reaction mixture was incubated for 10 minutes at 85° C. toinactivate the enzyme. 5 μL (5 pmol) of the crude circularsingle-stranded DNA were converted into the concatemeric pre-selectionlibraries with the illustra TempliPhi Amplification Kit (GE Healthcare)according to the manufacturer's protocol. Concatemeric pre-selectionlibraries were quantified with the Quant-it PicoGreen dsDNA Assay Kit(Invitrogen).

In Vitro Cleavage of on-Target and Off-Target Substrates.

Plasmid templates for PCR were constructed by ligation of annealedoligonucleotides CLTA(#) site fwd/rev into HindIII/XbaI double-digestedpUC19 (NEB). On-target substrate DNAs were generated by PCR with theplasmid templates and test fwd and test rev primers, then purified withthe QIAquick PCR Purification Kit (Qiagen). Off-target substrate DNAswere generated by primer extension. 100 pmol off-target (#) fwd andoff-target (#) rev primers were incubated at 95° C. and cooled at 0.1°C./s to 37° C. in NEBuffer2 (50 mM sodium chloride, 10 mM Tris-HCl, 10mM magnesium chloride, 1 mM dithiothreitol, pH 7.9) supplemented with 10μM dNTP mix (Bio-Rad). 10 U of Klenow Fragment (3′→5′ exo-) (NEB) wereadded to the reaction mixture and double-stranded off-target templateswere obtained by overlap extension for 1 h at 37° C. followed by enzymeinactivation for 20 min at 75° C., then purified with the QIAquick PCRPurification Kit (Qiagen). 200 nM substrate DNAs were incubated with 100nM Cas9 and 100 nM (v1.0 or v2.1) sgRNA or 1000 nM Cas9 and 1000 nM(v1.0 or v2.1) sgRNA in Cas9 cleavage buffer (200 mM HEPES, pH 7.5, 1.5M potassium chloride, 100 mM magnesium chloride, 1 mM EDTA, 5 mMdithiothreitol) for 10 min at 37° C. On-target cleavage reactions werepurified with the QIAquick PCR Purification Kit (Qiagen), and off-targetcleavage reactions were purified with the QIAquick Nucleotide RemovalKit (Qiagen) before electrophoresis in a Criterion 5% polyacrylamide TBEgel (Bio-Rad).

In Vitro Selection.

200 nM concatemeric pre-selection libraries were incubated with 100 nMCas9 and 100 nM sgRNA or 1000 nM Cas9 and 1000 nM sgRNA in Cas9 cleavagebuffer (200 mM HEPES, pH 7.5, 1.5 M potassium chloride, 100 mM magnesiumchloride, 1 mM EDTA, 5 mM dithiothreitol) for 10 min at 37° C.Pre-selection libraries were also separately incubated with 2 U of BspMIrestriction endonuclease (NEB) in NEBuffer 3 (100 mM NaCl, 50 mMTris-HCl, 10 mM MgCl2, 1 mM dithiothreitol, pH 7.9) for 1 h at 37° C.Blunt-ended post-selection library members or sticky-ended pre-selectionlibrary members were purified with the QIAQuick PCR Purification Kit(Qiagen) and ligated to 10 pmol adapter1/2(AACA) (Cas9:v2.1 sgRNA, 100nM), adapter1/2(TTCA) (Cas9:v2.1 sgRNA, 1000 nM), adapter1/2 (Cas9:v2.1sgRNA, 1000 nM), or lib adapter1/CLTA(#) lib adapter 2 (pre-selection)with 1,000 U of T4 DNA Ligase (NEB) in NEB T4 DNA Ligase Reaction Buffer(50 mM Tris-HCl, pH 7.5, 10 mM magnesium chloride, 1 mM ATP, 10 mMdithiothreitol) overnight (>10 h) at room temperature. Adapter-ligatedDNA was purified with the QIAquick PCR Purification Kit andPCR-amplified for 10-13 cycles with Phusion Hot Start Flex DNAPolymerase (NEB) in Buffer HF (NEB) and primers CLTA(#) sel PCR/PE2short (post-selection) or CLTA(#) lib seq PCR/lib fwd PCR(pre-selection). Amplified DNAs were gel purified, quantified with theKAPA Library Quantification Kit-Illumina (KAPA Biosystems), andsubjected to single-read sequencing on an Illumina MiSeq or Rapid Runsingle-read sequencing on an Illumina HiSeq 2500 (Harvard University FASCenter for Systems Biology Core facility, Cambridge, Mass.).

Selection Analysis.

Pre-selection and post-selection sequencing data were analyzed aspreviously described²¹, with modification (Algorithms) using scriptswritten in C++. Raw sequence data is not shown; see Table 2 for acurated summary. Specificity scores were calculated with the formulae:positive specificity score=(frequency of base pair atposition[post-selection]−frequency of base pair atposition[pre-selection])/(1−frequency of base pair atposition[pre-selection]) and negative specificity score=(frequency ofbase pair at position[post-selection]−frequency of base pair atposition[pre-selection])/(frequency of base pair atposition[pre-selection]). Normalization for sequence logos was performedas previously described²².

Cellular Cleavage Assays.

HEK293T cells were split at a density of 0.8×10⁵ per well (6-well plate)before transcription and maintained in Dulbecco's modified eagle medium(DMEM) supplemented with 10% fetal bovine serum (FBS) in a 37° C.humidified incubator with 5% CO₂. After 1 day, cells were transientlytransfected using Lipofectamine 2000 (Invitrogen) following themanufacturer's protocols. HEK293T cells were transfected at 70%confluency in each well of 6-well plate with 1.0 μg of the Cas9expression plasmid (Cas9-HA-2×NLS-GFP-NLS) and 2.5 μg of thesingle-strand RNA expression plasmid pSiliencer-CLTA (version 1.0 or2.1). The transfection efficiencies were estimated to be ˜70%, based onthe fraction of GFP-positive cells observed by fluorescence microscopy.48 h after transfection, cells were washed with phosphate bufferedsaline (PBS), pelleted and frozen at −80° C. Genomic DNA was isolatedfrom 200 μL cell lysate using the DNeasy Blood and Tissue Kit (Qiagen)according to the manufacturer's protocol.

Off-Target Site Sequence Determination.

100 ng genomic DNA isolated from cells treated with Cas9 expressionplasmid and single-strand RNA expression plasmid (treated cells) or Cas9expression plasmid alone (control cells) were amplified by PCR with 10 s72° C. extension for 35 cycles with primers CLTA(#)-(#)-(#) fwd andCLTA(#)-(#)-(#) rev and Phusion Hot Start Flex DNA Polymerase (NEB) inBuffer GC (NEB), supplemented with 3% DMSO. Relative amounts of crudePCR products were quantified by gel, and Cas9-treated (control) andCas9:sgRNA-treated PCRs were separately pooled in equimolarconcentrations before purification with the QIAquick PCR PurificationKit (Qiagen). Purified DNA was amplified by PCR with primersPE1-barcode# and PE2-barcode# for 7 cycles with Phusion Hot Start FlexDNA Polymerase (NEB) in Buffer HF (NEB). Amplified control and treatedDNA pools were purified with the QIAquick PCR Purification Kit (Qiagen),followed by purification with Agencourt AMPure XP (Beckman Coulter).Purified control and treated DNAs were quantified with the KAPA LibraryQuantification Kit-Illumina (KAPA Biosystems), pooled in a 1:1 ratio,and subjected to paired-end sequencing on an Illumina MiSeq.

Statistical Analysis.

Statistical analysis was performed as previously described²¹. P-valuesin Table 1 and Table 6 were calculated for a one-sided Fisher exacttest.

Algorithms

All scripts were written in C++. Algorithms used in this study are asprevious reported (reference) with modification.

Sequence binning.

1) designate sequence pairs starting with the barcode “AACA” or “TTCA”as post-selection library members. 2) for post-selection library members(with illustrated example):

Example Read:

(SEQ ID NO: 42) AACA CATGGGTCGACACAAACACAA CTCGGCAGGTACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAA CTCGGCAGGTATCTCGTATGCCi) search both paired reads for the positions, pos1 and pos2, of theconstant sequence “CTCGGCAGGT” (SEQ ID NO:43). ii) keep only sequencesthat have identical sequences between the barcode and pos1 and precedingpos2. iii) keep the region between the two instances of the constantsequence (the region between the barcode and pos1 contains a cuthalf-site; the region that is between the two instances of the constantsequence contains a full site)

Example:

(SEQ ID NO: 44) ACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAAii) search the sequence for a selection barcode (“TGTGTTTGTGTT” (SEQ IDNO:45) for CLTA1, “AGAAGAAGAAGA” (SEQ ID NO:46) for CLTA2,“TTCTCTTTCTCT” (SEQ ID NO:47) for CLTA3, “ACACAAACACAA” (SEQ ID NO:48)for CLTA4)

Example:

(SEQ ID NO: 49) ACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAA- CLTA4iii) the sequence before the barcode is the full post-selection librarymember (first four and last four nucleotides are fully randomizedflanking sequence)

Example:

(SEQ ID NO: 50) ACTT GCAGATGTAGTCTTTCCACATGG GTCG

iv) parse the quality scores for the positions corresponding to the 23nucleotide post-selection library member

Example Read:

(SEQ ID NO: 51) AACACATGGGTCGACACAAACACAACTCGGCAGGTACTTGCAGATGTAGTCTTTCCACATGGGTCGACACAAACACAACTCGGCAGGTATCTCGTATGCCCCCFFFFFHHHHHJJJJJJJJJJJJJJJJJJJJJGIJJJJIJIJJJIIIHIIJJJHHHGHAEFCDDDDDDDDDDDDDDDDDDDDDDD?CDDEDD @DCCCDv) keep sequences only if the corresponding quality score string(underlined) FASTQ quality characters for the sequence are ‘?’ or higherin ASCII code (Phred quality score >=30)

NHEJ Sequence Calling

Example Read:

(SEQ ID NO: 52) CAATCTCCCGCATGCGCTCAGTCCTCATCTCCCTCAAGCAGGCCCCGCTGGTGCACTGAAGAGCCA CCCTGTGAAACACTACATCTGC AATATCTTAATCCTACTCAGTGAAGCTCTTCACAGTCATTGGATTAATTATGTTGAGTTCTT TTGGACCAAACC

Example Quality Scores:

CCBCCFFFFCCCGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHGGGGGGGGGHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHFHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH HHHGHFHHHHHF1) identify the 20 base pairs flanking both sides of 20 base pair targetsite+three base pair PAM for each target site

Example Flanking Sequences:

(SEQ ID NO: 53) GCTGGTGCACTGAAGAGCCA (SEQ ID NO: 54)AATATCTTAATCCTACTCAG2) search all sequence reads for the flanking sequences to identify thepotential off-target site (the sequence between the flanking sequences)

Example Potential Off-Target Site:

(SEQ ID NO: 55) CCCTGTGAAACACTACATCTGC3) if the potential off-target site contains indels (length is less than23), keep sequence as potential off-target site if all correspondingFASTQ quality characters for the sequence are ‘?’ or higher in ASCIIcode (Phred quality score >=30)

Example Potential Off-Target Site Length=22

example corresponding FASTQ quality characters: HHGHHHHHHHHHHHHHHHHHHH

4) bin and manually inspect all sequences that pass steps 2 and 3 andkeep sequences as potential modified sequences if they have at least onedeletion involving position 16, 17, or 18 (of 20 counting from thenon-PAM end) of if they have an insertion between position 17 and 18,consistent with the most frequent modifications observed for theintended target site (FIG. 3)Example Potential Off-Target Site (Reverse Complement, with PositionsLabeled) with Reference Sequence:

                     11111111112222 non-PAM end 12345678901234567890123PAM end       GCAGATGTAGTGTTTC-ACAGGG (SEQ ID NO: 56)      GCAGATGTAGTGTTTCCACAGGG (SEQ ID NO: 57)4) repeat steps 1-3 for read2 and keep only if the sequence is the same5) compare overall counts in Cas9+sgRNA treated sample to Cas9 alonesample to identify modified sites

Filter Based on Cleavage Site (for Post-Selection Sequences)

1) tabulate the cleavage site locations across the recognition site byidentifying the first position in the full sequenced recognition site(between the two constant sequences) that is identical to the firstposition in the sequencing read after the barcode (before the firstconstant sequence).

2) after tabulation, repeat step 1, keeping only sequences with cleavagesite locations that are present in at least 5% of the sequencing reads.

Results Broad Off-Target DNA Cleavage Profiling Reveals RNA ProgrammedCas9 Nuclease Specificity.

Sequence-specific endonucleases including zinc-finger nucleases (ZFNs)and transcription activator-like effector nucleases (TALENs) have becomeimportant tools to modify genes in induced pluripotent stem cells(iPSCs),¹⁻³ in multi-cellular organisms,⁴⁻⁸ and in ex vivo gene therapyclinical trials.^(9, 10) Although ZFNs and TALENs have proved effectivefor such genetic manipulation, a new ZFN or TALEN protein must begenerated for each DNA target site. In contrast, the RNA-guided Cas9endonuclease uses RNA:DNA hybridization to determine target DNA cleavagesites, enabling a single monomeric protein to cleave, in principle, anysequence specified by the guide RNA.¹¹

Previous studies¹²⁻¹⁷ demonstrated that Cas9 mediates genome editing atsites complementary to a 20-nucleotide sequence in a bound guide RNA. Inaddition, target sites must include a protospacer adjacent motif (PAM)at the 3′ end adjacent to the 20-nucleotide target site; forStreptococcus pyogenes Cas9, the PAM sequence is NGG. Cas9-mediated DNAcleavage specificity both in vitro and in cells has been inferredpreviously based on assays against small collections of potentialsingle-mutation off-target sites. These studies suggested that perfectcomplementarity between guide RNA and target DNA is required in the 7-12base pairs adjacent to the PAM end of the target site (3′ end of theguide RNA) and mismatches are tolerated at the non-PAM end (5′ end ofthe guide RNA).^(11, 12, 17-19)

Although such a limited number of nucleotides specifying Cas9:guide RNAtarget recognition would predict multiple sites of DNA cleavage ingenomes of moderate to large size (>˜10⁷ bp), Cas9:guide RNA complexeshave been successfully used to modify both cells^(12, 13, 15) andorganisms.¹⁴ A study using Cas9:guide RNA complexes to modify zebrafishembryos observed toxicity at a rate similar to that of ZFNs andTALENs.¹⁴ A recent, broad study of the specificity of DNA binding(transcriptional repression) in E. coli of a catalytically inactive Cas9mutant using high-throughput sequencing found no detectable off-targettranscriptional repression in the relatively small E. colitranscriptome.²⁰ While these studies have substantially advanced ourbasic understanding of Cas9, a systematic and comprehensive profile ofCas9:guide RNA-mediated DNA cleavage specificity generated frommeasurements of Cas9 cleavage on a large number of related mutant targetsites has not been described. Such a specificity profile is needed tounderstand and improve the potential of Cas9:guide RNA complexes asresearch tools and future therapeutic agents.

We modified our previously published in vitro selection,²¹ adapted toprocess the blunt-ended cleavage products produced by Cas9 compared tothe overhang-containing products of ZFN cleavage, to determine theoff-target DNA cleavage profiles of Cas9:single guide RNA (sgRNA)¹¹complexes. Each selection experiment used DNA substrate librariescontaining ˜10¹² sequences, a size sufficiently large to includeten-fold coverage of all sequences with eight or fewer mutationsrelative to each 22-base pair target sequence (including the two-basepair PAM) (FIG. 1). We used partially randomized nucleotide mixtures atall 22 target-site base pairs to create a binomially distributed libraryof mutant target sites with an expected mean of 4.62 mutations pertarget site. In addition, target site library members were flanked byfour fully randomized base pairs on each side to test for specificitypatterns beyond those imposed by the canonical 20-base pair target siteand PAM.

Pre-selection libraries of 10¹² individual potential off-target siteswere generated for each of four different target sequences in the humanclathrin light chain A (CLTA) gene (FIG. 3). Synthetic 5′-phosphorylated53-base oligonucleotides were self-ligated into circular single-strandedDNA in vitro, then converted into concatemeric 53-base pair repeatsthrough rolling-circle amplification. The resulting pre-selectionlibraries were incubated with their corresponding Cas9:sgRNA complexes.Cleaved library members containing free 5′ phosphates were separatedfrom intact library members through the 5′ phosphate-dependent ligationof non-phosphorylated double-stranded sequencing adapters. Theligation-tagged post-selection libraries were amplified by PCR. The PCRstep generated a mixture of post-selection DNA fragments containing 0.5,1.5, or 2.5, etc. repeats of library members cleaved by Cas9, resultingfrom amplification of an adapter-ligated cut half-site with or withoutone or more adjacent corresponding full sites (FIG. 1). Post-selectionlibrary members with 1.5 target-sequence repeats were isolated by gelpurification and analyzed by high-throughput sequencing. In a finalcomputational selection step to minimize the impact of errors during DNAamplification or sequencing, only sequences with two identical copies ofthe repeated cut half-site were analyzed.

Pre-selection libraries were incubated under enzyme-limiting conditions(200 nM target site library, 100 nM Cas9:sgRNA v2.1) orenzyme-saturating conditions (200 nM target site library, 1000 nMCas9:sgRNA v2.1) for each of the four guide RNAs targets tested (CLTA1,CLTA2, CLTA3, and CLTA4) (FIGS. 3C and 3D). A second guide RNAconstruct, sgRNA v1.0, which is less active than sgRNA v2.1, was assayedunder enzyme-saturating conditions alone for each of the four guide RNAtargets tested (200 nM target site library, 1000 nM Cas9:sgRNA v1.0).The two guide RNA constructs differ in their length (FIG. 3) and intheir DNA cleavage activity level under the selection conditions,consistent with previous reports¹⁵ (FIG. 4). Both pre-selection andpost-selection libraries were characterized by high-throughput DNAsequencing and computational analysis. As expected, library members withfewer mutations were significantly enriched in post-selection librariesrelative to pre-selection libraries (FIG. 5).

Pre- and Post-Selection Library Composition.

The pre-selection libraries for CLTA1, CLTA2, CLTA3, and CLTA4 hadobserved mean mutation rates of 4.82 (n=1,129,593), 5.06 (n=847,618),4.66 (n=692,997), and 5.00 (n=951,503) mutations per 22-base pair targetsite, including the two-base pair PAM, respectively. The post-selectionlibraries treated under enzyme-limiting conditions with Cas9 plus CLTA1,CLTA2, CLTA3, or CLTA4 v.2.1 sgRNAs contained means of 1.14(n=1,206,268), 1.21 (n=668,312), 0.91 (n=1,138,568), and 1.82(n=560,758) mutations per 22-base pair target site. Under enzyme-excessconditions, the mean number of mutations among sequences survivingselection increased to 1.61 (n=640,391), 1.86 (n=399,560), 1.46(n=936,414), and 2.24 (n=506,179) mutations per 22-base pair targetsite, respectively, for CLTA1, CLTA2, CLTA3, or CLTA4 v2.1 sgRNAs. Theseresults reveal that the selection significantly enriched library memberswith fewer mutations for all Cas9:sgRNA complexes tested, and thatenzyme-excess conditions resulted in the putative cleavage of morehighly mutated library members compared with enzyme-limiting conditions(FIG. 5).

We calculated specificity scores to quantify the enrichment level ofeach base pair at each position in the post-selection library relativeto the pre-selection library, normalized to the maximum possibleenrichment of that base pair. Positive specificity scores indicate basepairs that were enriched in the post-selection library and negativespecificity scores indicate base pairs that were de-enriched in thepost-selection library. For example, a score of +0.5 indicates that abase pair is enriched to 50% of the maximum enrichment value, while ascore of −0.5 indicates that a base pair is de-enriched to 50% of themaximum de-enrichment value.

In addition to the two base pairs specified by the PAM, all 20 basepairs targeted by the guide RNA were enriched in the sequences from theCLTA1 and CLTA2 selections (FIG. 2, FIGS. 6 and 9, and Table 2). For theCLTA3 and CLTA4 selections (FIGS. 7 and 8, and Table 2), guideRNA-specified base pairs were enriched at all positions except for thetwo most distal base pairs from the PAM (5′ end of the guide RNA),respectively. At these non-specified positions farthest from the PAM, atleast two of the three alternate base pairs were nearly as enriched asthe specified base pair. Our finding that the entire 20 base-pair targetsite and two base pair PAM can contribute to Cas9:sgRNA DNA cleavagespecificity contrasts with the results from previous single-substrateassays suggesting that only 7-12 base pairs and two base pair PAM arespecified.^(11, 12, 15)

All single-mutant pre-selection (n≧14,569) and post-selection librarymembers (n≧103,660) were computationally analyzed to provide a selectionenrichment value for every possible single-mutant sequence. The resultsof this analysis (FIG. 2 and FIGS. 6 and 8) show that when onlysingle-mutant sequences are considered, the six to eight base pairsclosest to the PAM are generally highly specified and the non-PAM end ispoorly specified under enzyme-limiting conditions, consistent withprevious findings.^(11, 12, 17-19) Under enzyme-saturating conditions,however, single mutations even in the six to eight base pairs mostproximal to the PAM are tolerated, suggesting that the high specificityat the PAM end of the DNA target site can be compromised when enzymeconcentrations are high relative to substrate (FIG. 2). The observationof high specificity against single mutations close to the PAM onlyapplies to sequences with a single mutation and the selection results donot support a model in which any combination of mutations is toleratedin the region of the target site farthest from the PAM (FIG. 10-15).Analyses of pre- and post-selection library composition are describedelsewhere herein, position-dependent specificity patterns areillustrated in FIGS. 18-20, PAM nucleotide specificity is illustrated inFIGS. 21-24, and more detailed effects of Cas9:sgRNA concentration onspecificity are described in FIG. 2G and FIG. 25).

Specificity at the Non-PAM End of the Target Site.

To assess the ability of Cas9:v2.1 sgRNA under enzyme-excess conditionsto tolerate multiple mutations distal to the PAM, we calculated maximumspecificity scores at each position for sequences that containedmutations only in the region of one to 12 base pairs at the end of thetarget site most distal from the PAM (FIG. 10-17).

The results of this analysis show no selection (maximum specificityscore ˜0) against sequences with up to three mutations, depending on thetarget site, at the end of the molecule farthest from the PAM when therest of the sequence contains no mutations. For example, when only thethree base pairs farthest from the PAM are allowed to vary (indicated bydark bars in FIG. 11C) in the CLTA2 target site, the maximum specificityscores at each of the three variable positions are close to zero,indicating that there was no selection for any of the four possible basepairs at each of the three variable positions. However, when the eightbase pairs farthest from the PAM are allowed to vary (FIG. 11H), themaximum specificity scores at positions 4-8 are all greater than +0.4,indicating that the Cas9:sgRNA has a sequence preference at thesepositions even when the rest of the substrate contains preferred,on-target base pairs.

We also calculated the distribution of mutations (FIG. 15-17), in bothpre-selection and v2.1 sgRNA-treated post-selection libraries underenzyme-excess conditions, when only the first 1-12 base pairs of thetarget site are allowed to vary. There is significant overlap betweenthe pre-selection and post-selection libraries for only a subset of thedata (FIG. 15-17, a-c), demonstrating minimal to no selection in thepost-selection library for sequences with mutations only in the firstthree base pairs of the target site. These results collectively showthat Cas9:sgRNA can tolerate a small number of mutations (˜one to three)at the end of the sequence farthest from the PAM when provided withmaximal sgRNA:DNA interactions in the rest of the target site.

Specificity at the PAM End of the Target Site.

We plotted positional specificity as the sum of the magnitudes of thespecificity scores for all four base pairs at each position of eachtarget site, normalized to the same sum for the most highly specifiedposition (FIG. 18-20). Under both enzyme-limiting and enzyme-excessconditions, the PAM end of the target site is highly specified. Underenzyme-limiting conditions, the PAM end of the molecule is almostabsolutely specified (specificity score ≧+0.9 for guide RNA-specifiedbase pairs) by CLTA1, CTLA2, and CLTA3 guide RNAs (FIG. 2 and FIG. 6-9),and highly specified by CLTA4 guide RNA (specificity score of +0.7 to+0.9). Within this region of high specificity, specific singlemutations, consistent with wobble pairing between the guide RNA andtarget DNA, that are tolerated. For example, under enzyme-limitingconditions for single-mutant sequences, a dA:dT off-target base pair anda guide RNA-specified dG:dC base pair are equally tolerated at position17 out of 20 (relative to the non-PAM end of the target site) of theCLTA3 target site. At this position, an rG:dT wobble RNA:DNA base pairmay be formed, with minimal apparent loss of cleavage activity.

Importantly, the selection results also reveal that the choice of guideRNA hairpin affects specificity. The shorter, less-active sgRNA v1.0constructs are more specific than the longer, more-active sgRNA v2.1constructs when assayed under identical, enzyme-saturating conditionsthat reflect an excess of enzyme relative to substrate in a cellularcontext (FIG. 2 and FIGS. 5-8). The higher specificity of sgRNA v1.0over sgRNA v2.1 is greater for CLTA1 and CLTA2 (˜40-90% difference) thanfor CLTA3 and CLTA4 (<40% difference). Interestingly, this specificitydifference is localized to different regions of the target site for eachtarget sequence (FIGS. 2H and 26). Collectively, these results indicatethat different guide RNA architectures result in different DNA cleavagespecificities, and that guide RNA-dependent changes in specificity donot affect all positions in the target site equally. Given the inverserelationship between Cas9:sgRNA concentration and specificity describedabove, we speculate that the differences in specificity between guideRNA architectures arises from differences in their overall level ofDNA-cleavage activities.

Effects of Cas9:sgRNA Concentration on DNA Cleavage Specificity.

To assess the effect of enzyme concentration on patterns of specificityfor the four target sites tested, we calculated theconcentration-dependent difference in positional specificity andcompared it to the maximal possible change in positional specificity(FIG. 25). In general, specificity was higher under enzyme-limitingconditions than enzyme-excess conditions. A change from enzyme-excess toenzyme-limiting conditions generally increased the specificity at thePAM end of the target by ≧80% of the maximum possible change inspecificity. Although a decrease in enzyme concentration generallyinduces small (˜30%) increases in specificity at the end of the targetsites farthest from the PAM, concentration decreases induce much largerincreases in specificity at the end of the target site nearest the PAM.For CLTA4, a decrease in enzyme concentration is accompanied by a small(˜30%) decrease in specificity at some base pairs near the end of thetarget site farthest from the PAM.

Specificity of PAM Nucleotides.

To assess the contribution of the PAM to specificity, we calculated theabundance of all 16 possible PAM dinucleotides in the pre-selection andpost-selection libraries, considering all observed post-selection targetsite sequences (FIG. 21) or considering only post-selection target sitesequences that contained no mutations in the 20 base pairs specified bythe guide RNA (FIG. 22). Considering all observed post-selection targetsite sequences, under enzyme-limiting conditions, GG dinucleotidesrepresented 99.8%, 99.9%, 99.8%, and 98.5% of the post-selection PAMdinucleotides for selections with CLTA1, CLTA2, CLTA3, and CLTA4 v2.1sgRNAs, respectively. In contrast, under enzyme-excess conditions, GGdinucleotides represented 97.7%, 98.3%, 95.7%, and 87.0% of thepost-selection PAM dinucleotides for selections with CLTA1, CLTA2,CLTA3, and CLTA4 v2.1 sgRNAs, respectively. These data demonstrate thatan increase in enzyme concentration leads to increased cleavage ofsubstrates containing non-canonical PAM dinucleotides.

To account for the pre-selection library distribution of PAMdinucleotides, we calculated specificity scores for the PAMdinucleotides (FIG. 23). When only on-target post-selection sequencesare considered under enzyme-excess conditions (FIG. 24), non-canonicalPAM dinucleotides with a single G rather than two Gs are relativelytolerated. Under enzyme-excess conditions, Cas9:CLTA4 sgRNA 2.1exhibited the highest tolerance of non-canonical PAM dinucleotides ofall the Cas9:sgRNA combinations tested. AG and GA dinucleotides were themost tolerated, followed by GT, TG, and CG PAM dinucleotides. Inselections with Cas9:CLTA1, 2, or 3 sgRNA 2.1 under enzyme-excessconditions, AG was the predominate non-canonical PAM (FIGS. 23 and 24).Our results are consistent with another recent study of PAM specificity,which shows that Cas9:sgRNA can recognize AG PAM dinucleotides²³. Inaddition, our results show that under enzyme-limiting conditions, GG PAMdinucleotides are highly specified, and under enzyme-excess conditions,non-canonical PAM dinucleotides containing a single G can be tolerated,depending on the guide RNA context.

To confirm that the in vitro selection results accurately reflect thecleavage behavior of Cas9 in vitro, we performed discrete cleavageassays of six CLTA4 off-target substrates containing one to threemutations in the target site. We calculated enrichment values for allsequences in the post-selection libraries for the Cas9:CLTA4 v2.1 sgRNAunder enzyme-saturating conditions by dividing the abundance of eachsequence in the post-selection library by the calculated abundance inthe pre-selection library. Under enzyme-saturating conditions, thesingle one, two, and three mutation sequences with the highestenrichment values (27.5, 43.9, and 95.9) were cleaved to ≧71% completion(FIG. 27). A two-mutation sequence with an enrichment value of 1.0 wascleaved to 35%, and a two-mutation sequence with an enrichment valuenear zero (0.064) was not cleaved. The three-mutation sequence, whichwas cleaved to 77% by CLTA4 v2.1 sgRNA, was cleaved to a lowerefficiency of 53% by CLTA4 v1.0 sgRNA (FIG. 28). These results indicatethat the selection enrichment values of individual sequences arepredictive of in vitro cleavage efficiencies.

To determine if results of the in vitro selection and in vitro cleavageassays pertain to Cas9:guide RNA activity in human cells, we identified51 off-target sites (19 for CLTA1 and 32 for CLTA4) containing up toeight mutations that were both enriched in the in vitro selection andpresent in the human genome (Tables 3-5). We expressed Cas9:CLTA1 sgRNAv1.0, Cas9:CLTA1 sgRNA v2.1, Cas9:CLTA4 sgRNA v1.0, Cas9:CLTA4 sgRNAv2.1, or Cas9 without sgRNA in HEK293T cells by transient transfectionand used genomic PCR and high-throughput DNA sequencing to look forevidence of Cas9:sgRNA modification at 46 of the 51 off-target sites aswell as at the on-target loci; no specific amplified DNA was obtainedfor five of the 51 predicted off-target sites (three for CLTA1 and twofor CLTA4).

Deep sequencing of genomic DNA isolated from HEK293T cells treated withCas9:CLTA1 sgRNA or Cas9:CLTA4 sgRNA identified sequences evident ofnon-homologous end-joining (NHEJ) at the on-target sites and at five ofthe 49 tested off-target sites (CLTA1-1-1, CLTA1-2-2, CLTA4-3-1,CLTA4-3-3, and CLTA4-4-8) (Tables 1 and 6-8). The CLTA4 target site wasmodified by Cas9:CLTA4 v2.1 sgRNA at a frequency of 76%, whileoff-target sites, CLTA4-3-1 CLTA4-3-3, and CLTA4-4-8, were modified atfrequencies of 24%, 0.47% and 0.73%, respectively. The CLTA1 target sitewas modified by Cas9:CLTA1 v2.1 sgRNA at a frequency of 0.34%, whileoff-target sites, CLTA1-1-1 and CLTA1-2-2, were modified at frequenciesof 0.09% and 0.16%, respectively.

Under enzyme-saturating conditions with the v2.1 sgRNA, the two verifiedCLTA1 off-target sites, CLTA1-1-1 and CLTA1-2-2, were two of the threemost highly enriched sequences identified in the in vitro selection.CLTA4-3-1 and CLTA4-3-3 were the highest and third-highest enrichedsequences of the seven CLTA4 three-mutation sequences enriched in the invitro selection that are also present in the genome. The in vitroselection enrichment values of the four-mutation sequences were notcalculated, since 12 out of the 14 CLTA4 sequences in the genomecontaining four mutations, including CLTA4-4-8, were observed at a levelof only one sequence count in the post-selection library. Takentogether, these results confirm that several of the off-targetsubstrates identified in the in vitro selection that are present in thehuman genome are indeed cleaved by Cas9:sgRNA complexes in human cells,and also suggest that the most highly enriched genomic off-targetsequences in the selection are modified in cells to the greatest extent.

The off-target sites we identified in cells were among the most-highlyenriched in our in vitro selection and contain up to four mutationsrelative to the intended target sites. While it is possible thatheterochromatin or covalent DNA modifications could diminish the abilityof a Cas9:guide RNA complex to access genomic off-target sites in cells,the identification of five out of 49 tested cellular off-target sites inthis study, rather than zero or many, strongly suggests thatCas9-mediated DNA cleavage is not limited to specific targeting of onlya 7-12-base pair target sequence, as suggested in recentstudies.^(11, 12, 19)

The cellular genome modification data are also consistent with theincrease in specificity of sgRNA v1.0 compared to sgRNA v2.1 sgRNAsobserved in the in vitro selection data and discrete assays. Althoughthe CLTA1-2-2, CLTA 4-3-3, and CLTA 4-4-8 sites were modified by theCas9-sgRNA v2.1 complexes, no evidence of modification at any of thesethree sites was detected in Cas9:sgRNA v1.0-treated cells. The CLTA4-3-1site, which was modified at 32% of the frequency of on-target CLTA4 sitemodification in Cas9:v2.1 sgRNA-treated cells, was modified at only 0.5%of the on-target modification frequency in v1.0 sgRNA-treated cells,representing a 62-fold change in selectivity. Taken together, theseresults demonstrate that guide RNA architecture can have a significantinfluence on Cas9 specificity in cells. Our specificity profilingfindings present an important caveat to recent and ongoing efforts toimprove the overall DNA modification activity of Cas9:guide RNAcomplexes through guide RNA engineering.^(11, 15)

Overall, the off-target DNA cleavage profiling of Cas9 and subsequentanalyses show that (i) Cas9:guide RNA recognition extends to 18-20specified target site base pairs and a two-base pair PAM for the fourtarget sites tested; (ii) increasing Cas9:guide RNA concentrations candecrease DNA-cleaving specificity in vitro; (iii) using more activesgRNA architectures can increase DNA-cleavage specificity both in vitroand in cells but impair DNA-cleavage specificity both in vitro and incells; and (iv) as predicted by our in vitro results, Cas9:guide RNA canmodify off-target sites in cells with up to four mutations relative tothe on-target site. Our findings provide key insights to ourunderstanding of RNA-programmed Cas9 specificity, and reveal apreviously unknown role for sgRNA architecture in DNA-cleavagespecificity. The principles revealed in this study may also apply toCas9-based effectors engineered to mediate functions beyond DNAcleavage.

EQUIVALENTS AND SCOPE

Those skilled in the art will recognize, or be able to ascertain usingno more than routine experimentation, many equivalents to the specificembodiments of the invention described herein. The scope of the presentinvention is not intended to be limited to the above description, butrather is as set forth in the appended claims.

In the claims articles such as “a,” “an,” and “the” may mean one or morethan one unless indicated to the contrary or otherwise evident from thecontext. Claims or descriptions that include “or” between one or moremembers of a group are considered satisfied if one, more than one, orall of the group members are present in, employed in, or otherwiserelevant to a given product or process unless indicated to the contraryor otherwise evident from the context. The invention includesembodiments in which exactly one member of the group is present in,employed in, or otherwise relevant to a given product or process. Theinvention also includes embodiments in which more than one, or all ofthe group members are present in, employed in, or otherwise relevant toa given product or process.

Furthermore, it is to be understood that the invention encompasses allvariations, combinations, and permutations in which one or morelimitations, elements, clauses, descriptive terms, etc., from one ormore of the claims or from relevant portions of the description isintroduced into another claim. For example, any claim that is dependenton another claim can be modified to include one or more limitationsfound in any other claim that is dependent on the same base claim.Furthermore, where the claims recite a composition, it is to beunderstood that methods of using the composition for any of the purposesdisclosed herein are included, and methods of making the compositionaccording to any of the methods of making disclosed herein or othermethods known in the art are included, unless otherwise indicated orunless it would be evident to one of ordinary skill in the art that acontradiction or inconsistency would arise.

Where elements are presented as lists, e.g., in Markush group format, itis to be understood that each subgroup of the elements is alsodisclosed, and any element(s) can be removed from the group. It is alsonoted that the term “comprising” is intended to be open and permits theinclusion of additional elements or steps. It should be understood that,in general, where the invention, or aspects of the invention, is/arereferred to as comprising particular elements, features, steps, etc.,certain embodiments of the invention or aspects of the inventionconsist, or consist essentially of, such elements, features, steps, etc.For purposes of simplicity those embodiments have not been specificallyset forth in haec verba herein. Thus for each embodiment of theinvention that comprises one or more elements, features, steps, etc.,the invention also provides embodiments that consist or consistessentially of those elements, features, steps, etc.

Where ranges are given, endpoints are included. Furthermore, it is to beunderstood that unless otherwise indicated or otherwise evident from thecontext and/or the understanding of one of ordinary skill in the art,values that are expressed as ranges can assume any specific value withinthe stated ranges in different embodiments of the invention, to thetenth of the unit of the lower limit of the range, unless the contextclearly dictates otherwise. It is also to be understood that unlessotherwise indicated or otherwise evident from the context and/or theunderstanding of one of ordinary skill in the art, values expressed asranges can assume any subrange within the given range, wherein theendpoints of the subrange are expressed to the same degree of accuracyas the tenth of the unit of the lower limit of the range.

In addition, it is to be understood that any particular embodiment ofthe present invention may be explicitly excluded from any one or more ofthe claims. Where ranges are given, any value within the range mayexplicitly be excluded from any one or more of the claims. Anyembodiment, element, feature, application, or aspect of the compositionsand/or methods of the invention, can be excluded from any one or moreclaims. For purposes of brevity, all of the embodiments in which one ormore elements, features, purposes, or aspects is excluded are not setforth explicitly herein.

TABLES

Table 1. Cellular modification induced by Cas9:CLTA4 sgRNA.

33 human genomic DNA sequences were identified that were enriched in theCas9:CLTA4 v2.1 sgRNA in vitro selections under enzyme-limiting orenzyme-saturating conditions. Sites shown with underline containinsertions or deletions (indels) that are consistent with significantCas9:sgRNA-mediated modification in HEK293T cells. In vitro enrichmentvalues for selections with Cas9:CLTA4 v1.0 sgRNA or Cas9:CLTA4 v2.1sgRNA are shown for sequences with three or fewer mutations. Enrichmentvalues were not calculated for sequences with four or more mutations dueto low numbers of in vitro selection sequence counts. Modificationfrequencies (number of sequences with indels divided by total number ofsequences) in HEK293T cells treated with Cas9 without sgRNA (“nosgRNA”), Cas9 with CLTA4 v1.0 sgRNA, or Cas9 with CLTA4 v2.1 sgRNA.P-values are listed for those sites that show significant modificationin v1.0 sgRNA- or v2.1 sgRNA-treated cells compared to cells treatedwith Cas9 without sgRNA. “Not tested (n.t.)” indicates that PCR of thegenomic sequence failed to provide specific amplification products.

Table 2: Raw Selection Sequence Counts.

Positions −4 to −1 are the four nucleotides preceding the 20-base pairtarget site. PAM1, PAM2, and PAM3 are the PAM positions immediatelyfollowing the target site. Positions+4 to +7 are the four nucleotidesimmediately following the PAM.

Table 3: CLTA1 Genomic Off-Target Sequences.

20 human genomic DNA sequences were identified that were enriched in theCas9:CLTA1 v2.1 sgRNA in vitro selections under enzyme-limiting orenzyme-excess conditions. “m” refers to number of mutations fromon-target sequence with mutations shown in lower case. Sites shown withunderline contain insertions or deletions (indels) that are consistentwith significant Cas9:sgRNA-mediated modification in HEK293T cells.Human genome coordinates are shown for each site (assembly GRCh37).CLTA1-0-1 is present at two loci, and sequence counts were pooled fromboth loci. Sequence counts are shown for amplified and sequenced DNA foreach site from HEK293T cells treated with Cas9 without sgRNA (“nosgRNA”), Cas9 with CLTA1 v1.0 sgRNA, or Cas9 with CLTA1 v2.1 sgRNA.

Table 4: CLTA4 Genomic Off-Target Sequences.

33 human genomic DNA sequences were identified that were enriched in theCas9:CLTA4 v2.1 sgRNA in vitro selections under enzyme-limiting orenzyme-excess conditions. “m” refers to number of mutations fromon-target sequence with mutations shown in lower case. Sites shown withunderline contain insertions or deletions (indels) that are consistentwith significant Cas9:sgRNA-mediated modification in HEK293T cells.Human genome coordinates are shown for each site (assembly GRCh37).Sequence counts are shown for amplified and sequenced DNA for each sitefrom HEK293T cells treated with Cas9 without sgRNA (“no sgRNA”), Cas9with CLTA4 v1.0 sgRNA, or Cas9 with CLTA4 v2.1 sgRNA.

Table 5: Genomic Coordinates of CLTA1 and CLTA4 Off-Target Sites.

54 human genomic DNA sequences were identified that were enriched in theCas9:CLTA1 v2.1 sgRNA and Cas9:CLTA4 v2.1 sgRNA in vitro selectionsunder enzyme-limiting or enzyme-excess conditions. Human genomecoordinates are shown for each site (assembly GRCh37).

Table 6: Cellular Modification Induced by Cas9:CLTA1 sgRNA.

20 human genomic DNA sequences were identified that were enriched in theCas9:CLTA1 v2.1 sgRNA in vitro selections under enzyme-limiting orenzyme-excess conditions. Sites shown with underline contain insertionsor deletions (indels) that are consistent with significantCas9:sgRNA-mediated modification in HEK293T cells. In vitro enrichmentvalues for selections with Cas9:CLTA1 v1.0 sgRNA or Cas9:CLTA1 v2.1sgRNA are shown for sequences with three or fewer mutations. Enrichmentvalues were not calculated for sequences with four or more mutations dueto low numbers of in vitro selection sequence counts. Modificationfrequencies (number of sequences with indels divided by total number ofsequences) in HEK293T cells treated with Cas9 without sgRNA (“nosgRNA”), Cas9 with CLTA1 v1.0 sgRNA, or Cas9 with CLTA1 v2.1 sgRNA.P-values of sites that show significant modification in v1.0 sgRNA- orv2.1 sgRNA-treated cells compared to cells treated with Cas9 withoutsgRNA were 1.1E-05 (v1.0) and 6.9E-55 (v2.1) for CLTA1-0-1, 2.6E-03(v1.0) and 2.0E-10 (v2.1) for CLTA1-1-1, and 4.6E-08 (v2.1) forCLTA1-2-2. P-values were calculated using a one-sided Fisher exact test.“Not tested (n.t.)” indicates that the site was not tested or PCR of thegenomic sequence failed to provide specific amplification products.

Table 7: CLTA1 Genomic Off-Target Indel Sequences.

Insertion and deletion-containing sequences from cells treated withamplified and sequenced DNA for the on-target genomic sequence(CLTA1-0-1) and each modified off-target site from HEK293T cells treatedwith Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA1 v1.0 sgRNA, orCas9 with CLTA1 v2.1 sgRNA. “ref” refers to the human genome referencesequence for each site, and the modified sites are listed below.Mutations relative to the on-target genomic sequence are shown inlowercase letters. Insertions and deletions are shown in underlined boldletters or dashes, respectively. Modification percentages are shown forthose conditions (v1.0 sgRNA or v2.1 sgRNA) that show statisticallysignificant enrichment of modified sequences compared to the control (nosgRNA).

Table 8: CLTA4 Genomic Off-Target Indel Sequences.

Insertion and deletion-containing sequences from cells treated withamplified and sequenced DNA for the on-target genomic sequence(CLTA4-0-1) and each modified off-target site from HEK293T cells treatedwith Cas9 without sgRNA (“no sgRNA”), Cas9 with CLTA4 v1.0 sgRNA, orCas9 with CLTA4 v2.1 sgRNA. “ref” refers to the human genome referencesequence for each site, and the modified sites are listed below.Mutations relative to the on-target genomic sequence are shown inlowercase letters. Insertions and deletions are shown in underlined boldletters or dashes, respectively. Modification percentages are shown forthose conditions (v1.0 sgRNA or v2.1 sgRNA) that show statisticallysignificant enrichment of modified sequences compared to the control (nosgRNA).

Table 9: Oligonucleotides Used in this Study.

All oligonucleotides were purchased from Integrated DNA Technologies. Anasterisk (*) indicates that the preceding nucleotide was incorporated asa hand mix of phosphoramidites consisting of 79 mol % of thephosphoramidite corresponding to the preceding nucleotide and 4 mol % ofeach of the other three canonical phosphoramidites. “/SPhos/” denotes a5′ phosphate group installed during synthesis.

TABLE 1 in vitro # of enrichment Mutations sequence SEQ ID NO. gene v1.0v2.1 CLTA4-0-1 0 GCAGATGTAGTGTTTCCACAGGG SEQ ID NO: 58 CLTA 20     7.95CLTA4-3-1 3 aCAtATGTAGTaTTTCCACAGGG SEQ ID NO: 59 16.5   12.5  CLTA4-3-2 3 GCAtATGTAGTGTTTCCAaATGt SEQ ID NO: 60 2.99 6.97 CLTA4-3-3 3cCAGATGTAGTaTTcCCACAGGG SEQ ID NO: 61 CELF1 1.00 4.95 CLTA4-3-4 3GCAGtTtTAGTGTTTtCACAGGG SEQ ID NO: 62 BC073807 0.79 3.12 CLTA4-3-5 3GCAGAgtTAGTGTTTCCACACaG SEQ ID NO: 63 MPPED2 0    1.22 CLTA4-3-6 3GCAGATGgAGgGTTTtCACAGGG SEQ ID NO: 64 DCHS2 1.57 1.17 CLTA4-3-7 3GgAaATtTAGTGTTTCCACAGGG SEQ ID NO: 65 0.43 0.42 CLTA4-4-1 4aaAGAaGTAGTaTTTCCACATGG SEQ ID NO: 66 CLTA4-4-2 4aaAGATGTAGTcaTTCCACAAGG SEQ ID NO: 67 CLTA4-4-3 4aaAtATGTAGTcTTTCCACAGGG SEQ ID NO: 68 CLTA4-4-4 4atAGATGTAGTGTTTCCAaAGGa SEQ ID NO: 69 NR1H4 CLTA4-4-5 4cCAGAgGTAGTGcTcCCACAGGG SEQ ID NO: 70 CLTA4-4-6 4cCAGATGTgagGTTTCCACAAGG SEQ ID NO: 71 XKR6 CLTA4-4-7 4ctAcATGTAGTGTTTCCAtATGG SEQ ID NO: 72 HKR1 CLTA4-4-8 4ctAGATGaAGTGcTTCCACATGG SEQ ID NO: 73 CDK8 CLTA4-4-9 4GaAaATGgAGTGTTTaCACATGG SEQ ID NO: 74 CLTA4-4-10 4GCAaATGaAGTGTcaCCACAAGG SEQ ID NO: 75 CLTA4-4-11 4GCAaATGTAtTaTTTCCACtAGG SEQ ID NO: 76 NOV CLTA4-4-12 4GCAGATGTAGctTTTgtACATGG SEQ ID NO: 77 CLTA4-4-13 4GCAGcTtaAGTGTTTtCACATGG SEQ ID NO: 78 GRHL2 CLTA4-4-14 4ttAcATGTAGTGTTTaCACACGG SEQ ID NO: 79 LINC00535 CLTA4-5-1 5GaAGAgGaAGTGTTTgCcCAGGG SEQ ID NO: 80 RNH1 CLTA4-5-2 5GaAGATGTgGaGTTgaCACATGG SEQ ID NO: 81 FZD3 CLTA4-5-3 5GCAGAaGTAcTGTTgttACAAGG SEQ ID NO: 82 CLTA4-5-4 5GCAGATGTgGaaTTaCaACAGGG SEQ ID NO: 83 SLC9A2 CLTA4-5-5 5GCAGtcaTAGTGTaTaCACATGG SEQ ID NO: 84 CLTA4-5-6 5taAGATGTAGTaTTTCCAaAAGt SEQ ID NO: 85 CLTA4-6-1 6GCAGcTGgcaTtTcTCCACACGG SEQ ID NO: 86 CLTA4-6-2 6GgAGATcTgaTGgTTCtACAAGG SEQ ID NO: 87 CLTA4-6-3 6taAaATGcAGTGTaTCCAtATGG SEQ ID NO: 88 SMA4 CLTA4-7-1 7GCcagaaTAGTtTTTCaACAAGG SEQ ID NO: 89 SEPHS2 CLTA4-7-2 8ttgtATtTAGaGaTTgCACAAGG SEQ ID NO: 90 RORB modification frequency inHEK293T cells P-value no sgRNA v1.0 v2.1 v1.0 v2.1 CLTA4-0-1 0.021%  11%    76%  <1E−55 <1E−55 CLTA4-3-1 0.006% 0.055%     24% 6.0E−04<1E−55 CLTA4-3-2 0.017%    0% 0.014% CLTA4-3-3     0%    0% 0.469%2.5E−21  CLTA4-3-4     0%    0%     0% CLTA4-3-5 0.005% 0.015%  0.018%CLTA4-3-6 0.015% 0.023%  0.021% CLTA4-3-7 0.005% 0.012%  0.003%CLTA4-4-1 n.t. n.t. n.t. CLTA4-4-2 0.004%    0% 0.005% CLTA4-4-3 0.004%0.009%      0% CLTA4-4-4 0.032% 0.006%  0.052% CLTA4-4-5 0.005% 0.006% 0.007% CLTA4-4-6 0.018%    0% 0.007% CLTA4-4-7 0.006%    0% 0.008%CLTA4-4-8 0.009% 0.013% 0.730% 9.70E−21   CLTA4-4-9     0%    0% 0.004%CLTA4-4-10 0.004%    0%     0% CLTA4-4-11     0% 0.00%     0% CLTA4-4-12    0% 0.00%     0% CLTA4-4-13 0.020% 0.02% 0.030% CLTA4-4-14 n.t. n.t.n.t. CLTA4-5-1 0.004% 0.01% 0.006% CLTA4-5-2 0.004% 0.00%     0%CLTA4-5-3 0.002% 0.00% 0.003% CLTA4-5-4     0% 0.00%     0% CLTA4-5-50.004% 0.00% 0.005% CLTA4-5-6 0.007% 0.01%     0% CLTA4-6-1 n.t. n.t.n.t. CLTA4-6-2 0.007% 0.00% 0.009% CLTA4-6-3 0.015% 0.00%     0%CLTA4-7-1     0% 0.00% 0.007% CLTA4-7-2     0% 0.00%     0%

TABLE 2 100 nM Cas9:CLTA1 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 78 9 10 11 12 A 212906 240335 195549 240068 1.04E+06 72751 40206 6297241734 17376 18710 1.17E+06 24455 83195 46083 33528 C 285295 248395263973 260202 37925 32496 24822 1.10E+06 1.12E+06 42444 1.16E+06  533922096 1.06E+06 48105 1.14E+06 G 214213 219078 220275 189578 610621.04E+06 25785 11117  9125  5423  5745  5121  8080 14905  8906  3732 T493854 498460 526471 516420 64694 59173 1.12E+06 35336 34236 1.14E+0620532 24018 1.15E+06 50488 1.10E+06 32417 1000 nM Cas9:CLTA1 v1.0 sgRNAposition −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 154613 184336 154288177436 805105  66777  43354  56461  32941  15531  19465 904223  19696 56566  35200  26674 C 227144 201856 215667 220894  30269  30133  24249825333 865486  35164 889622  5488  17340 828521  36975 876790 G 163868174062 177891 148150  47940 784264  26342  17972  10299  6332  5785 5938  9185  11560  10641  3020 T 389059 374430 386838 388204  51370 53510 840739  34918  25958 877657  19812  19035 888463  38037 851868 28200 1000 nM Cas9:CLTA1 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 78 9 10 11 12 A 104782 127116 103361 124521 554601  40232  29541  38710 23659  10435  11462 618404  14608  41826  27762  19590 C 154144 136337145670 146754  20057  19440  17922 569754 590426  25233 612203  3834 15297 561351  26392 592757 G 113998 119668 120741 103026  32861 547445 18468  9314  6346  3908  4295  3719  5851  10887  15360  5605 T 267467257270 270619 266090  32872  33274 574460  22613  19960 600815  12431 14434 604635  26327 570877  22439 CLTA1 pre−selection library position−4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 241543 217144 209045 198284943175 103452  76259 106919 124476  59762 108373 937511  65477 110282 67774  96299 C 254366 269805 276090 322860  52984  65855  58943 834238812029  52168 839963  54708  43285 831610  50109 861358 G 230024 196574210445 180859  60496 857631  66783  89366  85315  67098  77499  59257 71824  89579  68090  66121 T 403590 446000 433943 427520  72868 102585927538  99000 107703 950495 103688  78047 948937  98052 943550 105745100 nM Cas9:CLTA2 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 1011 12 A 109129 135587  94032 141748 5.74E+04  44802  48284 24464 1161116668 6282 6.58E+05 655917  28909  24210 656617 C 155710 138970 207735220443 529643  24503 566049 6.27E+05 6.46E+05 19040 6.52E+05 2351  25771.30E+04 617274 2.64E+03 G 136555 142038 118241 105620  39991 2.11E+04 26481  3756  3627  2889 2488 3025  3202 609865  8312  5889 T 266918251717 248304 200501  41277 577893 2.75E+04 13008  7318 6.30E+05 74874920 6.62E+03  16554 1.85E+04  3165 1000 nM Cas9:CLTA2 v1.0 sgRNAposition −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A  94138 115628  85485120676  52411  41438  46093  22399  9066  14310  5351 567337 565061 24132  23848 556483 C 140695 125708 179224 191394 452192  21517 481298538392 557549  16233 562576  1973  2127  11807 525901  4992 G 113243118054 101836  91048  35101  18969  22797  3440  2802  2960  2526  2895 2793 526655  9738  8100 T 228367 217053 209898 173125  36739 494519 26255  12212  7026 542940  5990  4238  6462  13849  16956  4868 1000 nMCas9:CLTA2 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 64249  81812  58977  85387  35172  29833  33434  19419  9272  13136 4907 391675 389930  19852  16657 383605 C  96983  67918 124642 127760316077  14548 327166 364874 380987  11360 387025  1694  1815  8124363374  5168 G  77913  80500  68612  64299  23522  15748  19664  3856 3035  2752  2062  2398  2439 360755  7431  6019 T 160415 149330 147329122114  24789 339431  19296  11411  6266 372312  5566  3793  5376  10829 12098  4768 CLTA2 pre−selection library position −4 −3 −2 −1 1 2 3 4 56 7 8 9 10 11 12 A 203147 173899 167999 170203  89970  73770  88239 88611  76114  78589  75016 726091 712150  96111  90307 728931 C 181430214835 246369 272618 632831  41977 641062 644565 670872  40877 649838 38931  44961  46591 628706  32296 G 177090 153006 151178 140868  58664 49976  60827  56077  52341  49259  55484  39801  38939 630670  55013 38368 T 285951 305878 282072 263929  66153 681895  57490  58365  48291678893  67280  42795  51838  74246  73592  48023 100 nM Cas9:CLT3A v2.1sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 212836 248582202151 249368 9.13E+04 77392 19048  39738 1078520 1106930  461961.12E+06  64461 11912 30992  21158 C 233270 241259 274819 305120  3789435918 13930 5.61E+03 1.22E+04   3774 6.35E+03  4063   6018 1.11E+0627501 4.68E+04 G 211701 187534 185281 196614  66632 9.88E+05 265721074020  12936   9205 1066570  7418 1050360  3828  3949   2231 T 480761461193 476317 387466 942707 37284 1.08E+06  19204  34885 1.87E+04  1945011145 1.77E+04 13689 1.08E+06 1068370 1000 nM Cas9:CLTA3 v1.0 sgRNAposition −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 219833 263464 207913264018  97886  78562  20663  39724 1136320 1151200  42966 1156400  49443 18669  44652  44644 C 240570 261247 311444 333414  39996  40484  13961  5323  11099   5475  10323   6501   8456 1126310  36792  56203 G 221683206195 199246 215583  76580 1032080  24785 1126840  12654  12465 1114450 12075 1113930  12078  19275   9014 T 506611 457791 470094 375682 974235 37571 1129290  16811  28626  19560  20956  13723  16864  31636 10879801078840 1000 nM Cas9:CLTA3 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 78 9 10 11 12 A 169775 206549 166197 201768  75243  67150  20449  36549876154 898360  39901 911344  44415  13218  37301  33080 C 197800 209445243688 264177  32775  34540  14250  7885  14793  4878  7791  4636  7510890591  28425  46269 G 174766 158928 158824 168325  58121 801768  26558866689  13343  12052 868394  8837 867980  7923  14022  6553 T 394073361492 367705 302144 770275  32956 875157  25291  32124  21124  20328 11597  16509  24682 856666 850512 CLTA3 pre-selection library position−4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 173122 135327 138244 142599 50365  69486  37040  66315 575295 566722  70249 528947  72610  41265 61770  56547 C 143788 158534 162646 177240  25902  40142  28129  34668 38933  36129  61591  52201  46032 559715  32233  34830 G 137601 132826130592 128304  42860 534378  42217 531723  29873  34068 479149  49753501888  41949  43243  30118 T 238486 266310 261515 244854 573870  48991585611  60291  48896  56078  82008  62096  72467  50068 555751 571502100 nM Cas9:CLTA4 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 1011 12 A  55030  78101  78867  81833 8.09E+04  58148 525585  29962 54491819446  54151 2.59E+04 550200  29521  34194  38891 C 168401 162082 139480130495  22088 428628  4498 1.21E+04 5.14E+03 15601 7.10E+03  35217  24812.35E+04  16846 2.03E+04 G  89302  75785  82959 133275 415632 4.70E+04 14868 504358  6156  9951 493432  14899  4528 498832  27411 497382 T248025 244790 259452 215155  42090  26956 1.58E+04  14300  4541 5.16E+05 6071 484788 3.55E+03  8877 4.82E+05  4222 1000 nM Cas9:CLTA4 v1.0 sgRNAposition −4 −3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A  95188 141261 145156141850 151224 116745 928773  50295 975924  29201  95476  30383 980248 50181  65094  77253 C 305024 297215 260676 243819  34420 745345  8606 17266  7541  29948  10779  47831  5069  32501  30389  29610 G 159888139073 153474 225343 742232  85777  29776 907007  9285  13455 883325 19640  8303 902733  44730 879985 T 438973 421524 439767 388061  71197 51206  31918  24505  6323 926469  9493 901219  5453  13658 858860 12225 1000 nM Cas9:CLTA4 v2.1 sgRNA position −4 −3 −2 −1 1 2 3 4 5 6 78 9 10 11 12 A  47674  70467  71535  72698  72554  54587 471218  27627493315  16818  47470  17728 498471  29769  40021  41618 C 154985 151636133622 122579  18730 384037  4452  10916  4303  16232  5436  28594  1961 19017  19152  18001 G  80869  69972  76726 118084 379024  42360  14989453870  5084  6863 448784  10260  3281 450120  23076 439828 T 222651214104 224296 192818  35871  25195  15520  13766  3477 466266  4489449597  2466  7273 423930  6732 CLTA4 pre−selection library position −4−3 −2 −1 1 2 3 4 5 6 7 8 9 10 11 12 A 106798 131577 131941 132368 127160103294 820923 103844 840417  99163 133349 123366 824537 126564 115133122618 C 304597 297419 277233 283453  50833 722264  29748  65558  44890 59551  73916  77470  45318  84973  73106  90384 G 146240 137027 134399183111 695802  68240  51484 708098  30709  62837  67352  89897  49093672860  88125 663922 T 393868 385480 407930 352571  77708  57705  49348 74003  35487 729952  70486 660770  32555  67106 675139  74579 100 nMCas9:CLTA1 v2.1 sgRNA position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4+5 +6 +7 A  8551  9668 4582 32237 1.19E+06 1.20E+06 2032 4237 2610561386 574 235167 223887 222343 301956 C 1.14E+06 1.18E+06 4090 1.13E+064363  628  969 1.19E+06 210095  167 152 211027 273777 264354 309690 G 3294  3867 3597  7260 3400 2474 1.19E+06 1301 238989 1.20E+06 1.21E+06205765 222282 240526 217260 T 57980 13065 1.19E+06 36826 8959 3966 93548065 496128  475 211 554309 486322 479045 377362 1000 nM Cas9:CLTA1 v1.0sgRNA position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A 7925  9269  4859  32891 910633 925527  3595  5976 183479  1390   413182704 171051 174062 221899 C 880022 908816  4419 859691  5694   776 2120 920211 180463   120   88 180657 220438 211411 245967 G  2819  3185 2994  6763  3631  2894 916417  1415 193418 932808 934044 172551 172071176484 161703 T  43918  13414 922412  35339 14726  5487  12552  7082377324   366   139 398772 371124 372727 305115 1000 nM Cas9:CLTA1 v2.1sgRNA position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A 8961  19434  9549  35083 604115 607264  4665  16515 125225  10391  2519125288 114575 120476 149847 C 594469 616112  11645 553993  13212  4438 5146 590160 116022   329   138 123802 154249 146572 166531 G  3378 3517  5896  22551  8658  12770 613580  3712 121392 628464 637588 118800113560 118464 111278 T  33583  1328 613301  28764  14406  15919  17000 30004 277752  1207   146 272501 258007 254879 212735 CLTA1pre−selection library position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4+5 +6 +7 A  88029 109977  62686 119399 931093 908362  64248 111479190574  97896 104002 183367 178912 198049 219754 C 841819 817157  51676797914  60106  52998  42317 813253 239201  56843  59450 289074 295400289007 284268 G  86080  96496  81367 104949  52143  77389 918970  96000192652 879150 870948 196672 202194 196499 202544 T 113595 105893 933794107261  86181  90774 103988 108791 507096  95634  95123 460410 453017445968 422957 100 nM Cas9:CLTA2 v2.1 sgRNA position 13 14 15 16 17 18 1920 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  59160  36601  2974 12980 3.27E+031.09E+03 17686  689 193742 284 129 143150 165553 136708 146056 C1.48E+04 9.12E+03 660929 6.50E+05 660305 666122  1314 6.65E+05  42664 48  43 162563 111729 143442 177253 G 581322 606454  1564  2134  1819  89 6.44E+05  505 137388 6.68E+05 6.68E+05 103305 146355 139972 124772T  13024  16134 2.85E+03  3253  2918  1016  4886 2608 294518 146  42259294 244675 248190 220231 1000 nM Cas9:CLTA2 v1.0 sgRNA position 13 1415 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  49577  39401  5425 30774  6408  5055  36081  2573 148145   782   243 132801 126862 118528122897 C  13617  13316 563557 535780 560658 567693  4938 569653  46472  70   45 133402 123970 130555 148756 G 495156 496382  1789  3325  1846  166 519782   520 125177 575395 576103 118877 108849 104210 103370 T 18093  27344  5672  6564  7531  3529  15642  3697 256649   196   52191363 216762 223150 201420 1000 nM Cas9:CLTA2 v2.1 sgRNA position 13 1415 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  32780  22855  9722 25181  12518  17950  28198  5471 100745  4933   834  89339  87351 82615  85108 C  9569  9710 374342 355544 373485 370343  11652 378841 40532   238   34  93621  87920  91380 105625 G 344511 350245  1559 5882  1339   391 331376  1034  74803 393760 398660  79776  75927  74068 70435 T  12700  16750  13937  12953  12218  10876  28334  14214 183480  629   32 136824 148362 151497 138392 CLTA2 pre−selection libraryposition 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  91515 84764  79586  86205  87337  85547  92983 100316 177716  84144  88017177831 180209 176904 174190 C  49519  46571 641958 624548 637703 635473 51727 594349 136372  41282  41689 216880 206368 210039 235263 G 627263642878  59549  55292  53056  57979 616575  66553 158929 656315 654970162242 160704 157741 138890 T  79321  73405  66525  81573  69522  68619 86333  86400 374601  65877  62942 290665 300337 302934 299275 100 nMCas9:CLT3A v2.1 sgRNA position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4+5 +6 +7 A 6465 1130430   4097   5750 7.71E+04 1.14E+06 6151   2047305062 1993 394 213566 240851 230230 252637 C 1.12E+06 1.96E+03 11294001.82E+03   3421  167 1451 6.66E+02 261609  103  82 319990 253055 261338293644 G 2504   2471   1726   2881 1081680  876 1.13E+06   600 2288651.14E+06 1.14E+06 142425 192720 220683 227840 T 9829   3709 3.34E+031128120   6398 1320 4480 1135260 343032  211  69 462587 451942 426317364447 1000 nM Cas9:CLTA3 v1.0 sgRNA position 13 14 15 16 17 18 19 20PAM1 PAM2 PAM3 +4 +5 +6 +7 A  44771 1152540  16264  30980  71714 1156700 47106  27658 276285  36304  12701 219034 239515 244440 255360 C 1096280  8437 1156840   8448  25120   4351  24685   9473 297135   1331   939354289 298216 277740 292917 G   7707   9466   2708  17195 1053760  102781085310  10308 238545 1148550 1174510 171862 193096 217301 239319 T 39940  18250  12883 1132070  38103  17372  31596 1141260 376732   2514  550 443512 457870 449216 401101 1000 nM Cas9:CLTA3 v2.1 sgRNA position13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  26409 893670  6315 20807  52541 903619  33690  20904 205940  26623  9880 172210 182986187305 196429 C 870864  7991 910584  5931  19923  4977  18171  6508229797  1163   693 283240 240802 224453 236469 G  3393  7912  1499 12906 836022  9011 859600  8302 190011 906628 925513 132620 153591172169 187623 T  35748  26841  18016 896770  27928  18807  24953 900700310666  2000   328 348344 359035 352487 315893 CLTA3 pre-selectionlibrary position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A 75555 586476  61203  51740  70943 569277  70484  50807 130402  57527 61702 110207 118993 126967 127707 C 519328  30904 540977  24982  45344 35359  44014  35778 174938  42259  46083 201434 190347 184768 207347 G 38922  34282  34082  37275 515778  36956 516177  45203 137307 539445527404 113323 119846 118423 127230 T  59192  41335  56735 579000  60932 51405  62322 561209 250350  53766  57808 268033 263811 262839 230713100 nM Cas9:CLTA4 v2.1 sgRNA position 13 14 15 16 17 18 19 20 PAM1 PAM2PAM3 +4 +5 +6 +7 A  26542  23991  15243  25122 5.36E+03 5.51E+05  1994540029  47731 4642 1401  77633  56902  63224  54815 C 3.69E+04 8.47E+03 5182 5.22E+05 547711  5715 546119 3.02E+03 152056  655  473 141123164035 146401 190955 G  6729  3344  3716  3926  3162   554 1.45E+03 4637  72296 5.55E+05 5.58E+05  84257  77627  75123  91454 T 490573524958 5.37E+05  9437  4528  3692  11194  13069 288675  911  495 257745262194 276010 223534 1000 nM Cas9:CLTA4 v1.0 sgRNA position 13 14 15 1617 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  42674  41050  32933  55244 39984 942989  19900 887311  80159  28536  12390 142460  96664 110844 99920 C  61641  25910  21400 887446 900777  34590 940504  23749 257985 2556  4791 252462 297152 258929 338099 G  16677  7879  8429  12432 17373  4103  7346  20095 139488 964013 976818 154302 139784 136512165750 T 878081 924234 936311  43951  40939  17391  31323  67918 521441 3968  5074 449849 465473 492788 395304 1000 nM Cas9:CLTA4 v2.1 sgRNAposition 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4 +5 +6 +7 A  24741 23050  16409  27974  2697 478335  12667 451298  36128  22041  16967 68943  49017  56451  51102 C  35213  12845  13497 445302 480543  15631469503  11832 122541  3529  8965 126313 153105 134293 171499 G  7741 5091  5456  7558  7112  3083  5302  10184  87517 474540 471647  85849 72063  71600  85239 T 438484 465193 470817  25345  15827  9130  18707 32865 259993  6069  8600 225074 231994 243835 198339 CLTA4pre−selection library position 13 14 15 16 17 18 19 20 PAM1 PAM2 PAM3 +4+5 +6 +7 A 108492 107761  96384  99908  76163 806675  75877 793806 87755  82110  83605 111015 103082 109315 101198 C  78280  76978  66776738550 776738  55522 754283  42188 278802  57603  55530 266156 281433258029 295144 G  67768  53472  58440  47550  41427  42574  54424  59162151536 740525 732891 163824 158224 146268 151560 T 696963 713292 729903 65495  57175  46732  66919  56347 433410  71265  79477 410508 408764437891 403601

TABLE 3 no sgRNA v1.0 sgRNA v2.1 sgRNA modified total modified totalmodified total m sequence sequences sequences sequences sequencessequences sequences CLTA1-0-1 0 AGTCCTCATCTCCCTCAAGCAGG 2 58889 18 42683 178   52845 (SEQ ID NO: 91) CLTA1-1-1 1 AGTCCTCAaCTCCCTCAAGCAGG 139804 9 29000 37  40588 (SEQ ID NO: 92) CLTA1-2-1 2AGcCCTCATtTCCCTCAAGCAGG 0 16276 0 15032 0 18277 (SEQ ID NO: 93)CLTA1-2-2 2 AcTCCTCATCcCCCTCAAGCCGG 3 21267 1 20042 33  22579 (SEQ IDNO: 94) CLTA1-2-3 2 AGTCaTCATCTCCCTCAAGCAGa 0     0 0     0 0     0 (SEQID NO: 95) CLTA1-3-1 3 cGTCCTCcTCTCCCcCAAGCAGG 2 53901 0 42194 0 52205(SEQ ID NO: 96) CLTA1-3-2 3 tGTCCTCtTCTCCCTCAAGCAGa 0 14890 0 14231 015937 (SEQ ID NO: 97) CLTA1-4-1 4 AagCtTCATCTCtCTCAAGCTGG 0 49579 231413 0 41234 (SEQ ID NO: 98) CLTA1-4-2 4 AGTaCTCtTtTCCCTCAgGCTGG 230013 1 23470 4 26999 (SEQ ID NO: 99) CLTA1-4-3 4AGTCtTaAatTCCCTCAAGCAGG 2 63792 0 52321 1 73007 (SEQ ID NO: 100)CLTA1-4-4 4 AGTgCTCATCTaCCagAAGCTGG 1 12585 0 11339 0 12066 (SEQ ID NO:101) CLTA1-4-5 4 ccTCCTCATCTCCCTgcAGCAGG 4 30568 1 23810 0 27870 (SEQ IDNO: 102) CLTA1-4-6 4 ctaCaTCATCTCCCTCAAGCTGG 0 13200 1 12886 2 12843(SEQ ID NO: 103) CLTA1-4-7 4 gGTCCTCATCTCCCTaAAaCAGa 1  8697 3  8188 0 8783 (SEQ ID NO: 104) CLTA1-4-8 4 tGTCCTCATCggCCTCAgGCAGG 0 13169 08805 2 12830 (SEQ ID NO: 105) CLTA1-5-1 5 AGaCacCATCTCCCTtgAGCTGG 046109 1 32515 2 35567 (SEQ ID NO: 106) CLTA1-5-2 5AGgCaTCATCTaCaTCAAGtTGG 0 41280 0 28896 0 35152 (SEQ ID NO: 107)CLTA1-5-3 5 AGTaaTCActTCCaTCAAGCCGG 0     0 0     0 0     0 (SEQ ID NO:108) CLTA1-5-4 5 tccCCTCAcCTCCCTaAAGCAGG 2 24169 5 17512 1 23483 (SEQ IDNO: 109) CLTA1-5-5 5 tGTCtTtATtTCCCTCtAGCTGG 0 11527 0 10481 1 11027(SEQ ID NO: 110) CLTA1-6-1 6 AGTCCTCATCTCCCTCAAGCAGG 0  6537 0  5654 0 6741 (SEQ ID NO: 111)

TABLE 4 no sgRNA v1.0 sgRNA v2.1 sgRNA modified total modified totalmodified total m sequence sequences sequences sequences sequencessequences sequences CLTA4-0-1 0 GCAGATGTAGTGTTTCCACAGGG 6 29191 2005   18640 14970     19661 (SEQ ID NO: 112) CLTA4-3-1 3aCAtATGTAGTaTTTCCACAGGG 2 34165 11  20018 3874    16082 (SEQ ID NO: 113)CLTA4-3-2 3 GCAtATGTAGTGTTTCCAaATGt 3 17923 0 11688 2 13880 (SEQ ID NO:114) CLTA4-3-3 3 cCAGATGTAGTaTTcCCACAGGG 0 16559 0 12007 52  11082 (SEQID NO: 115) CLTA4-3-4 3 GCAGtTtTAGTGTTTtCACAGGG 0 21722 0 12831 0 15726(SEQ ID NO: 116) CLTA4-3-5 3 GCAGAgtTAGTGTTTCCACACaG 1 21222 2 13555 316425 (SEQ ID NO: 117) CLTA4-3-6 3 GCAGATGgAGgGTTTtCACAGGG 3 20342 312804 3 14068 (SEQ ID NO: 118) CLTA4-3-7 3 GgAaATtTAGTGTTTCCACAGGG 238894 3 24017 1 29347 (SEQ ID NO: 119) CLTA4-4-1 4aaAGAaGTAGTaTTTCCACATGG 0     0 0     0 0     0 (SEQ ID NO: 120)CLTA4-4-2 4 aaAGATGTAGTcaTTCCACAAGG 1 27326 0 17365 1 18941 (SEQ ID NO:121) CLTA4-4-3 4 aaAtATGTAGTcTTTCCACAGGG 2 46232 3 32264 0 32638 (SEQ IDNO: 122) CLTA4-4-4 4 atAGATGTAGTGTTTCCAaAGGa 9 27821 1 16223 8 15388(SEQ ID NO: 123) CLTA4-4-5 4 cCAGAgGTAGTGcTcCCACAGGG 1 20979 1 15674 115086 (SEQ ID NO: 124) CLTA4-4-6 4 cCAGATGTgagGTTTCCACAAGG 4 22021 015691 1 14253 (SEQ ID NO: 125) CLTA4-4-7 4 ctAcATGTAGTGTTTCCAtATGG 235942 0 23076 1 11867 (SEQ ID NO: 126) CLTA4-4-8 4ctAGATGaAGTGcTTCCACATGG 1 10692 1  7609 59   8077 (SEQ ID NO: 127)CLTA4-4-9 4 GaAaATGgAGTGTTTaCACATGG 0 34616 0 22302 1 24671 (SEQ ID NO:128) CLTA4-4-10 4 GCAaATGaAGTGTcaCCACAAGG 1 25210 0 16187 0 16974 (SEQID NO: 129) CLTA4-4-11 4 GCAaATGTAtTaTTTCCACtAGG 0 34144 1 24770 0 22547(SEQ ID NO: 130) CLTA4-4-12 4 GCAGATGTAGctTTTgtACATGG 0 14254 0  9616 0 9994 (SEQ ID NO: 131) CLTA4-4-13 4 GCAGcTtaAGTGTTTtCACATGG 8 39466 17609 5 16525 (SEQ ID NO: 132) CLTA4-4-14 4 ttAcATGTAGTGTTTaCACACGG 0 0 022302 0 0 (SEQ ID NO: 133) CLTA4-5-1 5 GaAGAgGaAGTGTTTgCcCAGGG 1 27616 116319 1 16140 (SEQ ID NO: 134) CLTA4-5-2 5 GaAGATGTgGaGTTgaCACATGG 122533 0 14292 0 15013 (SEQ ID NO: 135) CLTA4-5-3 5GCAGAaGTAcTGTTgttACAAGG 1 44243 1 29391 1 29734 (SEQ ID NO: 136)CLTA4-5-4 5 GCAGATGTgGaaTTaCaACAGGG 0 27321 0 13640 0 14680 (SEQ ID NO:137) CLTA4-5-5 5 GCAGtcaTAGTGTaTaCACATGG 1 26538 0 18449 1 20559 (SEQ IDNO: 138) CLTA4-5-6 5 taAGATGTAGTaTTTCCAaAAGt 1 15145 1 8905 0  7911 (SEQID NO: 139) CLTA4-6-1 6 GCAGcTGgcaTtTcTCCACACGG 0     2 0     0 0     0(SEQ ID NO: 140) CLTA4-6-2 6 GgAGATcTgaTGgTTCtACAAGG 2 27797 0 19450 221709 (SEQ ID NO: 141) CLTA4-6-3 6 taAaATGcAGTGTaTCCAtATGG 4 27551 018424 0 18783 (SEQ ID NO: 142) CLTA4-7-1 7 GCcagaaTAGTtTTTCaACAAGG 020942 0 13137 1 13792 (SEQ ID NO: 143) CLTA4-7-2 8ttgtATtTAGaGaTTgCACAAGG 0 28470 0 18104 0 20416 (SEQ ID NO: 144)

TABLE 5 Off-target site Human genome coordinates CLTA1-0-1 9(+):36,211,732-36,211,754 12(+): 7,759,893-7,759,915 CLTA1-1-1 8(−):15,546,437-15,546,459 CLTA1-2-1 3(−): 54,223,111-54,223,133 CLTA1-2-215(+): 89,388,670-89,388,692 CLTA1-2-3 5(+): 88716920-88,716,942CLTA1-3-1 21(+): 27,972,462-27,972,484 CLTA1-3-2 4(−):17,179,924-17,179,946 CLTA1-4-1 1(+): 147,288,742-147,288,764 CLTA1-4-210(+): 97,544,444-97,544,466 CLTA1-4-3 2(−): 161,873,870-161,873,892CLTA1-4-4 1(+): 196,172,702-196,172,724 CLTA1-4-5 13(+):56,574,636-56,574,658 CLTA1-4-6 2(+): 241,357,827-241,357,849 CLTA1-4-73(+): 121,248,627-121,248,649 CLTA1-4-8 12(+): 132,937,319-132,937,341CLTA1-5-1 9(−): 80,930,919-80,930,941 CLTA1-5-2 2(+):140,901,875-14,0901,897 CLTA1-5-3 3(+): 45,016,841-45,016,863 CLTA1-5-4X(+): 40,775,684-40,775,706 CLTA1-5-5 2(−): 185,151,622-185,151,644CLTA1-6-1 X(+): 150,655,097-150,655,119 CLTA4-0-1 9(−):36,211,779-36,211,801 CLTA4-3-1 12(−): 50,679,419-50,679,441 CLTA4-3-2X(−): 143,939,483-143,939,505 CLTA4-3-3 11(−): 47,492,611-47,492,633CLTA4-3-4 3(−): 162,523,715-162,523,737 CLTA4-3-5 11(+):30,592,975-30,592,997 CLTA4-3-6 4(−): 155,252,699-155,252,721 CLTA4-3-718(+): 39,209,441-39,209,463 CLTA4-4-1 17(−): 36,785,650-36,785,672CLTA4-4-2 1(−): 241,537,119-241,537,141 CLTA4-4-3 8(−):120,432,103-120,432,125 CLTA4-4-4 6(−): 106,204,600-106,204,622CLTA4-4-5 8(+): 102,527,804-102,527,826 CLTA4-4-6 8(−):94,685,538-94,685,560 CLTA4-4-7 2(+): 35,820,054-35,820,076 CLTA4-4-83(−): 36,590,352-36,590,374 CLTA4-4-9 12(+): 100,915,498-100,915,520CLTA4-4-10 21(+): 33,557,705-33,557,727 CLTA4-4-11 8(+):10,764,183-10,764,205 CLTA4-4-12 19(+): 37,811,645-37,811,667 CLTA4-4-1313(−): 26,832,673-26,832,695 CLTA4-4-14 6(+): 19,349,572-19,349,594CLTA4-5-1 11(−): 502,300-502,322 CLTA4-5-2 8(−): 28,389,683-28,389,705CLTA4-5-3 2(−): 118,557,405-118,557,427 CLTA4-5-4 2(−):103,248,360-103,248,382 CLTA4-5-5 21(−): 42,929,085-42,929,107 CLTA4-5-613(−): 83,097,278-83,097,300 CLTA4-6-1 2(+): 43,078,423-43,078,445CLTA4-6-2 7(−): 11,909,384-11,909,406 CLTA4-6-3 5(−):69,775,482-69,775,504 CLTA4-7-1 16(+): 30,454,945-30,454,967 CLTA4-7-29(−): 77,211,328-77,211,350

TABLE 6 in vitro modification frequency number of enrichment in HEK293Tcells mutations sequence gene v1.0 v2.1 no sgRNA v1.0 v2.1 CLTA1-0-1 0AGTCCTCATCTCCCTCAAGCAGG CLTA 41.4 23.3   0.003% 0.042% 0.337% (SEQ IDNO: 145) CLTA1-1-1 1 AGTCCTCAaCTCCCTCAAGCAGG TUSC3 25.9 14     0.003%0.031% 0.091% (SEQ ID NO: 146) CLTA1-2-1 2 AGcCCTCATtTCCCTCAAGCAGGCACNA2D3 15.4 26.2       0%     0%     0% (SEQ ID NO: 147) CLTA1-2-2 2AcTCCTCATCcCCCTCAAGCCGG ACAN 29.2 18.8   0.014% 0.005% 0.146% (SEQ IDNO: 148) CLTA1-2-3 2 AGTCaTCATCTCCCTCAAGCAGa   0.06 1.27 n.t. n.t. n.t.(SEQ ID NO: 149) CLTA1-3-1 3 cGTCCTCcTCTCCCcCAAGCAGG 0  2.07 0.004%    0%     0% (SEQ ID NO: 150) CLTA1-3-2 3 tGTCCTCtTCTCCCTCAAGCAGaBC029598 0  1.47     0%     0%     0% (SEQ ID NO: 151) CLTA1-4-1 4AagCtTCATCTCtCTCAAGCTGG     0% 0.006%     0% (SEQ ID NO: 152) CLTA1-4-24 AGTaCTCtTtTCCCTCAgGCTGG ENTPD1 0.007% 0.004% 0.015% (SEQ ID NO: 153)CLTA1-4-3 4 AGTCtTaAatTCCCTCAAGCAGG 0.003%     0% 0.001% (SEQ ID NO:154) CLTA1-4-4 4 AGTgCTCATCTaCCagAAGCTGG 0.008%     0%     0% (SEQ IDNO: 155) CLTA1-4-5 4 ccTCCTCATCTCCCTgcAGCAGG 0.013% 0.004%     0% (SEQID NO: 156) CLTA1-4-6 4 ctaCaTCATCTCCCTCAAGCTGG     0% 0.008% 0.016%(SEQ ID NO: 157) CLTA1-4-7 4 gGTCCTCATCTCCCTaAAaCAGa POLQ (coding)0.011% 0.037%     0% (SEQ ID NO: 158) CLTA1-4-8 4tGTCCTCATCggCCTCAgGCAGG     0%     0% 0.016% (SEQ ID NO: 159) CLTA1-5-15 AGaCacCATCTCCCTtgAGCTGG PSAT1     0% 0.003% 0.006% (SEQ ID NO: 160)CLTA1-5-2 5 AGgCaTCATCTaCaTCAAGtTGG     0%     0%     0% (SEQ ID NO:161) CLTA1-5-3 5 AGTaaTCActTCCaTCAAGCCGG ZDHHC3, n.t. n.t. n.t. (SEQ IDNO: 162) EXOSC7 CLTA1-5-4 5 tccCCTCAcCTCCCTaAAGCAGG 0.008% 0.029% 0.004%(SEQ ID NO: 163) CLTA1-5-5 5 tGTCtTtATtTCCCTCtAGCTGG     0%     0%0.009% (SEQ ID NO: 164) CLTA1-6-1 6 AGTCCTCATCTCCCTCAAGCAGG     0%    0%     0% (SEQ ID NO: 165)

TABLE 7 # of sequences sequence no sgRNA v1.0 sgRNA v2.1 sgRNA CLTA1-0-1ref AGTCCTCATCTCCCTCAAGCAGG (SEQ ID 58,887 42,665 52,667 NO: 166)AGTCCTCATCTCCCTCA A AGCAGG (SEQ ID 0 0 66 NO: 167)AGTCCTCATCTCCCTC-AGCAGG (SEQ ID 0 2 28 NO: 168) AGTCCTCAT--------------0 0 13 AGTCCTCATCTCCCTCA T AGCAGG (SEQ ID 0 0 11 NO: 169)AGTCCTCAT--------AGCAGG (SEQ ID 0 0 9 NO: 170) AGTCCTCATCT------AGCAGG(SEQ ID 0 0 8 NO: 171) AGTCCTCA---------AGCAGG (SEQ ID 0 0 6 NO: 172)AGTCCTCATCTCCCTCA AAGGCAGTGTTTGTT 0 0 4 ACTTGAGTTTGTC AGCAGG (SEQ ID NO:173) AGTCCTCATCTCCCTCA TT AGCAGG (SEQ ID 0 0 4 NO: 174)AGTCCTCATCTCCCTCA GGGCTTGTTTACAGC 0 0 3 TCACCTTTGAATTTGCACAAGCGTGCAAGCAG G (SEQ ID NO: 175) AGTCCTCATCTCCCT-AGCAGG (SEQ ID 0 11 0 NO: 176)AGTCCTCATCCCTC-AAGCAGG (SEQ ID 0 3 0 NO: 177) AGTCCTCATCTCCCT-AAGCAGG(SEQ ID 1 2 0 NO: 178) other 1 0 26 modified total 2 18 178 (0.042%)(0.34%) CLTA1-1-1 ref AGTCCTCATCTCCCTCAAGCAGG (SEQ ID 39,803 28,99140,551 NO: 179) AGTCCTCAaCTCCCTCA A AGCAGG (SEQ ID 0 4 13 NO: 180)AGTCCTCAaCTCCCTCA------ (SEQ ID 0 0 12 NO: 181) AGTCCTCAaCTCCCTC-AGCAGG(SEQ ID 0 2 4 NO: 182) AGTCCTCAaCTCCCTCA AGAAAGGTGTTGAAAA 0 0 3TCAGAAAGAGAGAAACA AGCAGG (SEQ ID NO: 183) AGTCCTCAaCTCCCTCAATCTACGGTCCATTCC 0 0 2 CGTTTCCACTCACCTTGCGCCGC AGCAGG (SEQ ID NO: 184)AGTCCTCAaCTCCCT-AAGCAGG (SEQ ID 0 3 1 NO: 185) AGTCCTCAaCTCCCTCAACCAACTTTAACATCC 0 0 1 TGCTGGTTCTGTCATTAATAAGTTGAA AGCAGG (SEQ ID NO:186) AGTCCTCAaCTCCCTCA CAGCAAATAAAAAAGT 0 0 1 TGTTTATGCATATTCAGATAAGCAAAGCAGG (SEQ ID NO: 187) AGTCCTCAaCTCCC-AAGCAGG (SEQ ID 1 0 0 NO: 188)modified total 1 9 37 (0.031%) (0.091%) CLTA1-2-2 refAcTCCTCATCcCCCTCAAGCCGG (SEQ ID 21,264 20,041 22,546 NO: 189)AcTCCTCATCcCCCTCA A AGCCGG (SEQ ID 0 0 8 NO: 190) AcTCCTCATCcCCCTCA GAGCCGG (SEQ ID 0 0 7 NO: 191) AcTCCTC-----------AGCCGG (SEQ ID 0 0 5 NO:192) AcTCCTCATCcCCCTCA AA AGCCGG (SEQ ID 0 0 2 NO: 193)AcTCCTCATCcCCCTCA GC AGCCGG (SEQ ID 0 0 2 NO: 194) AcTCCTCATCcCCCTCA TAGCCGG (SEQ ID 0 0 2 NO: 195) AcTCCTCATCcCCCTCA TCC CCGG (SEQ ID 0 0 2NO: 196) AcTCCTCATCcC-----AGCCGG (SEQ ID 0 0 2 NO: 197)AcTCCTCATCcCCCTA-AGCCGG (SEQ ID 3 1 1 NO: 198) AcTCCTCATCcCCCTCA ATAGCCGG (SEQ ID 0 0 1 NO: 199) AcTCCTCACCcCCCTCA GC AGCCGG (SEQ ID 0 0 1NO: 200) modified total 3 1 33 (0.15%)

TABLE 8 # of sequences sequence control v1.0 sgRNA v2.1 sgRNA CLTA4-0-1ref GCAGATGTAGTGTTTCCACAGGG 29,185 16,635 17,555 (SEQ ID NO: 201)GCAGATGTAGTGTTTC-ACAGGG 1 891 5,937 (SEQ ID NO: 202) GCAGATGTAGTGTTTCC CACAGGG 0 809 5,044 (SEQ ID NO: 203) GCAGATGTAGTG----CACAGGG 0 14 400(SEQ ID NO: 204) GCAGATGTAGTGTTTCC-CAGGG 0 19 269 (SEQ ID NO: 205)GCAGATGTAC-------ACAGGG 0 17 262 (SEQ ID NO: 206)GCAGATGTAGTGTCA---CAGGG 2 6 254 (SEQ ID NO: 207) GCAGATGTAGTGTTCA-CAGGG(SEQ 0 21 229 ID NO: 208) GCAGATGTAGTGTTTC-CAGGG (SEQ 1 14 188 ID NO:209) GCAGATGTAGT-----CACAGGG 0 0 152 (SEQ ID NO: 210)GCAGATGT-----------AGGG 0 6 129 (SEQ ID NO: 211) other 2 208 2,106modified total 6 2,005 14,970   (11%)   (76%) CLTA4-3-1 refaCAtATGTAGTaTTTCCACAGGG 34,163 20,007 12,208 (SEQ ID NO: 212)aCAtATGTAGTaTTTCC C ACAGGG 0 8 1779 (SEQ ID NO: 213)aCAtATGTAGTaTTTCA-CAGGG 1 0 293 (SEQ ID NO: 214) aCAtATGTAGTaTTTC-CAGGG(SEQ 1 0 227 ID NO: 215) aCAtAT----------CACAGGG 0 0 117 (SEQ ID NO:216) a-----------------CAGGG 0 0 96 aCAt------------CACAGGG 0 0 78 (SEQID NO: 217) aCAtATGTAGT-----CACAGGG 0 0 77 (SEQ ID NO: 218)aCAtATGTAGTaTTTCC------ 0 0 76 (SEQ ID NO: 219) aCAtATGT-----------AGGG0 0 68 (SEQ ID NO: 220) aCAtATGTAG------CACAGGG 0 0 64 (SEQ ID NO: 221)other 0 3 999 modified total 2 11 3874 (0.055%)   (24%) CLTA4-3-3 refcCAGATGTAGTaTTcCCACAGGG 16,559 12,007 11,030 (SEQ ID NO: 222)cCAGATGTAGTaTTcCC C ACAGGG 0 0 35 (SEQ ID NO: 223)cCAGATGTAGTaT----ACAGGG 0 0 5 (SEQ ID NO: 224) cCAGATGTAGTaT---CACAGGG 00 3 (SEQ ID NO: 225) cCAGATGTAGTaTTcCC AAC ACAGGG 0 0 2 (SEQ ID NO: 226)cCAGATGTAGTaTT-CACAGGG (SEQ 0 0 2 ID NO: 227) cCAGATGTAGTaTTcC-CAGGG(SEQ 0 0 2 ID NO: 228) cCAGATGTA-------------- 0 0 2cCAGATGTAGTaTTcC-ACAGGG 0 0 1 (SEQ ID NO: 229) modified total 0 0 52(0.47%) CLTA4-4-8 ref ctAGATGaAGTGcTTCCACATGG 10,691 7,608 8,018 (SEQ IDNO: 230) ctAGATGaAGTGcTTCC C ACATGG 0 0 49 (SEQ ID NO: 231)ctAGATGaAGTGcTTC-ACATGG 0 0 6 (SEQ ID NO: 232) ctAGATGaAGTG----------- 00 2 (SEQ ID NO: 233) ctAGATGaAGTGcTTCCAC AC ATGG 0 0 1 (SEQ ID NO: 234)ctAGATGaAGTGcTTC-CATGG (SEQ 1 0 0 ID NO: 235) ctAGATGaAGTGcTTCC-CATGG 01 0 (SEQ ID NO: 236) modified total 1 1 59 (0.73%)

TABLE 9 oligonucleotide name oligonucleotide sequence (5′->3′) CLTA1v2.1 template fwd TAA TAC GAC TCA CTA TAG GAG TCC TCA TCT CCC TCA AGCGTT TTA GAG CTA TGC TG (SEQ ID NO: 237) CLTA2 v2.1 template fwd TAA TACGAC TCA CTA TAG GCT CCC TCA AGC AGG CCC CGC GTT TTA GAG CTA TGC TG (SEQID NO: 238) CLTA3 v2.1 template fwd TAA TAC GAC TCA CTA TAG GTG TGA AGAGCT TCA CTG AGT GTT TTA GAG CTA TGC TG (SEQ ID NO: 239) CLTA4 v2.1template fwd TAA TAC GAC TCA CTA TAG GGC AGA TGT AGT GTT TCC ACA GTT TTAGAG CTA TGC TG (SEQ ID NO: 240) v2.1 template rev GAT AAC GGA CTA GCCTTA TTT TAA CTT GCT ATG CTT TTC AGC ATA GCT CTA AAA C (SEQ ID NO: 241)CLTA1 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAAAAC GCT TGA GGG AGA TGA GGA CTC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 242)CLTA2 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAAAAC GCG GGG CCT GCT TGA GGG AGC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 243)CLTA3 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAAAAC ACT CAG TGA AGC TCT TCA CAC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 244)CLTA4 v1.0 template CGG ACT AGC CTT ATT TTA ACT TGC TAT TTC TAG CTC TAAAAC TGT GGA AAC ACT ACA TCT GCC CTA TAG TGA GTC GTA TTA (SEQ ID NO: 245)T7 promoter oligo TAA TAC GAC TCA CTA TAG G (SEQ ID NO: 246) CLTA1 lib/5Phos/AAC ACA NNN NC*C* NG*C* T*T*G* A*G*G* G*A*G* A*T*G* A*G*G* A*C*T*NNN NAC CTG CCG AGA ACA CA (SEQ ID NO: 247) CLTA2 lib /5Phos/TCT TCT NNNNC*C* NG*C* G*G*G* G*C*C* T*G*C* T*T*G* A*G*G* G*A*G* NNN NAC CTG CCGAGT CTT CT (SEQ ID NO: 248) CLTA3 lib /5Phos/AGA GAA NNN NC*C* NA*C*T*C*A* G*T*G* A*A*G* C*T*C* T*T*C* A*C*A* NNN NAC CTG CCG AGA GAG AA(SEQ ID NO: 249) CLTA4 lib /5Phos/TTG TGT NNN NC*C* NT*G* T*G*G* A*A*A*C*A*C* T*A*C* A*T*C* T*G*C* NNN NAC CTG CCG AGT TGT GT (SEQ ID NO: 250)CLTA1 site fwd CTA GCA GTC CTC ATC TCC CTC AAG CAG GC (SEQ ID NO: 251)CLTA1 site rev AGC TGC CTG CTT GAG GGA GAT GAG GAC TG (SEQ ID NO: 252)CLTA2 site fwd CTA GTC TCC CTC AAG CAG GCC CCG CTG GT (SEQ ID NO: 253)CLTA2 site rev AGC TAC CAG CGG GGC CTG CTT GAG GGA GA (SEQ ID NO: 254)CLTA3 site fwd CTA GCT GTG AAG AGC TTC ACT GAG TAG GA (SEQ ID NO: 255)CLTA3 site rev AGC TTC CTA CTC AGT GAA GCT CTT CAC AG (SEQ ID NO: 256)CLTA4 site fwd CTA GTG CAG ATG TAG TGT TTC CAC AGG GT (SEQ ID NO: 257)CLTA4 site rev AGC TAC CCT GTG GAA ACA CTA CAT CTG CA (SEQ ID NO: 258)test fwd GCG ACA CGG AAA TGT TGA ATA CTC AT (SEQ ID NO: 259) test revGGA GTC AGG CAA CTA TGG ATG AAC G (SEQ ID NO: 260) off-target CLTA4-0fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GCA GAT GTA GTG TTTCCA CAG GGT (SEQ ID NO: 261) off-target CLTA4-1 fwd ACT GTG AAG AGC TTCACT GAG TAG GAT TAA GAT ATT GAA GAT GTA GTG TTT CCA CAG GGT (SEQ ID NO:262) off-target CLTA4-2a fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GATATT GAA GAT GTA GTG TTT CCA CTG GGT (SEQ ID NO: 263) off-target CLTA4-2bfwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GAT ATT GCA GAT GGA GGG TTTCCA CAG GGT (SEQ ID NO: 264) off-target CLTA4-2c fwd ACT GTG AAG AGC TTCACT GAG TAG GAT TAA GAT ATT GCA GAT GTA GTG TTA CCA GAG GGT (SEQ ID NO:265) off-target CLTA4-3 fwd ACT GTG AAG AGC TTC ACT GAG TAG GAT TAA GATATT GGG GAT GTA GTG TTT CCA CTG GGT (SEQ ID NO: 266) off-target CLTA4-0rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CTG TGG AAA CACTAC ATC TGC (SEQ ID NO: 267) off-target CLTA4-1 rev TCC CTC AAG CAG GCCCCG CTG GTG CAC TGA AGA GCC ACC CTG TGG AAA CAC TAC ATC TTC (SEQ ID NO:268) off-target CLTA4-2a rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGAGCC ACC CAG TGG AAA CAC TAC ATC TTC (SEQ ID NO: 269) off-target CLTA4-2brev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGA GCC ACC CTG TGG AAA CCCTCC ATC TGC (SEQ ID NO: 270) off-target CLTA4-2c rev TCC CTC AAG CAG GCCCCG CTG GTG CAC TGA AGA GCC ACC CTC TGG TAA CAC TAC ATC TGC (SEQ ID NO:271) off-target CLTA4-3 rev TCC CTC AAG CAG GCC CCG CTG GTG CAC TGA AGAGCC ACC CAG TGG AAA CAC TAC ATC CCC (SEQ ID NO: 272) adapter1(AACA) AATGAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATCTAA CA (SEQ ID NO: 273) adapter2(AACA) TGT TAG ATC GGA AGA GCG TCG TGTAGG GAA AGA GTG TAG ATC TCG GTG G (SEQ ID NO: 274) adapter1(TTCA) AATGAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATCTTT CA (SEQ ID NO: 275) adapter2(TTCA) TGA AAG ATC GGA AGA GCG TCG TGTAGG GAA AGA GTG TAG ATC TCG GTG G (SEQ ID NO: 276) adapter1 AAT GAT ACGGCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATC T (SEQID NO: 277) adapter2 AGA TCG GAA GAG CGT CGT GTA GGG AAA GAG TGT AGA TCTCGG TGG (SEQ ID NO: 278) lib adapter1 GAC GGC ATA CGA GAT (SEQ ID NO:279) CLTA1 lib adapter2 AAC AAT CTC GTA TGC CGT CTT CTG CTT G (SEQ IDNO: 280) CLTA2 lib adapter2 TCT TAT CTC GTA TGC CGT CTT CTG CTT G (SEQID NO: 281) CLTA3 lib adapter2 AGA GAT CTC GTA TGC CGT CTT CTG CTT G(SEQ ID NO: 282) CLTA4 lib adapter2 TTG TAT CTC GTA TGC CGT CTT CTG CTTG (SEQ ID NO: 283) CLTA1 sel PCR CAA GCA GAA GAC GGC ATA CGA GAT TGT GTTCTC GGC AGG T (SEQ ID NO: 284) CLTA2 sel PCR CAA GCA GAA GAC GGC ATA CGAGAT AGA AGA CTC GGC AGG T (SEQ ID NO: 285) CLTA3 sel PCR CAA GCA GAA GACGGC ATA CGA GAT TTC TCT CTC GGC AGG T (SEQ ID NO: 286) CLTA4 sel PCR CAAGCA GAA GAC GGC ATA CGA GAT ACA CAA CTC GGC AGG T (SEQ ID NO: 287) PE2short AAT GAT ACG GCG ACC ACC GA (SEQ ID NO: 288) CLTA1 lib seq PCR AATGAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATCTNN NNA CCT ACC TGC CGA GAA CAC A (SEQ ID NO: 289) CLTA2 lib seq PCR AATGAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATCTNN NNA CCT ACC TGC CGA GTC TTC T (SEQ ID NO: 290) CLTA3 lib seq PCR AATGAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATCTNN NNA CCT ACC TGC CGA GAG AGA A (SEQ ID NO: 291) CLTA4 lib seq PCR AATGAT ACG GCG ACC ACC GAG ATC TAC ACT CTT TCC CTA CAC GAC GCT CTT CCG ATCTNN NNA CCT ACC TGC CGA GTT GTG T (SEQ ID NO: 292) lib fwd PCR CAA GCAGAA GAC GGC ATA CGA GAT (SEQ ID NO: 293) CLTA1-0-1 (Chr. 9) fwd ACA CTCTTT CCC TAC ACG ACG CTC TTC CGA TCT CAA GTC TAG CAA GCA GGC CA (SEQ IDNO: 294) CLTA1-0-1 (Chr. 12) fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGATCT CAG GCA CTG AGT GGG AAA GT (SEQ ID NO: 295) CLTA1-1-1 fwd ACA CTCTTT CCC TAC ACG ACG CTC TTC CGA TCT TAA CCC CAA GTC AGC AAG CA (SEQ IDNO: 296) CLTA1-2-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTGCTG GTC AAT ACC CTG GC (SEQ ID NO: 297) CLTA1-2-2 fwd ACA CTC TTT CCCTAC ACG ACG CTC TTC CGA TCT TGA GTA CCC CTG AAA TGG GC (SEQ ID NO: 298)CLTA1-3-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCG CTA CCAATC AGG GCT TT (SEQ ID NO: 299) CLTA1-3-2 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT CCA TTG CCA CTT GTT TGC AT (SEQ ID NO: 300)CLTA1-4-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCT ACC CCCACA ACT TTG CT (SEQ ID NO: 301) CLTA1-4-2 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT GTG TAC ATC CAG TGC ACC CA (SEQ ID NO: 302)CLTA1-4-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCG GAA AGGACT TTG AAT ACT TGT (SEQ ID NO: 303) CLTA1-4-4 fwd ACA CTC TTT CCC TACACG ACG CTC TTC CGA TCT CGG CCC AAG ACC TCA TTC AC (SEQ ID NO: 304)CLTA1-4-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GTC CTC TCTGGG GCA GAA GT (SEQ ID NO: 305) CLTA1-4-6 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT AGC TGA GTC ATG AGT TGT CTC C (SEQ ID NO: 306)CLTA1-4-7 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTG CCA GCTTCT CAC ACC AT (SEQ ID NO: 307) CLTA1-4-8 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT CTG AAG GAC AAA GGC GGG AA (SEQ ID NO: 308)CLTA1-5-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT AAG GTG CTAAAG GCT CCA CG (SEQ ID NO: 309) CLTA1-5-2 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT GAC CAT TGG TGA GCC CAG AG (SEQ ID NO: 310)CLTA1-5-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTT TTC GGGCAA CTG CTC AC (SEQ ID NO: 311) CLTA1-5-4 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT GCA AGC CTT CTC TCC TCA GA (SEQ ID NO: 312)CLTA1-5-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ACA CAA ACTTCC CTG AGA CCC (SEQ ID NO: 313) CLTA1-6-1 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TGA GTT AGC CCT GCT GTT CA (SEQ ID NO: 314)CLTA4-0-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGA AGA GCTTCA CTG AGT AGG A (SEQ ID NO: 315) CLTA4-3-1 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TCC CCT TAC AGC CAA TTT CGT (SEQ ID NO: 316)CLTA4-3-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGC TGA TGAAAT GCA ATT AAG AGG T (SEQ ID NO: 317) CLTA4-3-3 fwd ACA CTC TTT CCC TACACG ACG CTC TTC CGA TCT GGT CCC TGC AAG CCA GTA TG (SEQ ID NO: 318)CLTA4-3-4 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ATC AAA GCCTTG TAT CAC AGT T (SEQ ID NO: 319) CLTA4-3-5 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT CCC AAA TAA TGC AGG AGC CAA (SEQ ID NO: 320)CLTA4-3-6 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTG CCT TTAGTG GGA CAG ACT T (SEQ ID NO: 321) CLTA4-3-7 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT AGT AAC CCT AGT AGC CCT CCA (SEQ ID NO: 322)CLTA4-4-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CAT TGC AGTGAG CCG AGA TTG (SEQ ID NO: 323) CLTA4-4-2 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TGG CAA AGT TCA CTT CCA TGT (SEQ ID NO: 324)CLTA4-4-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TGC TCT GTGATG TCT GCC AC (SEQ ID NO: 325) CLTA4-4-4 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TGT GTA GGA TTG TGA ACC AGC A (SEQ ID NO: 326)CLTA4-4-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TCC CAG CCCAGC ATT TTT CT (SEQ ID NO: 327) CLTA4-4-6 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT AGG TTG CTT TGT GCA CAG TC (SEQ ID NO: 328)CLTA4-4-7 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCT GGC TTGGGA TGT TGG AA (SEQ ID NO: 329) CLTA4-4-8 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TTG CCC AAG GTC ATA CTG CT (SEQ ID NO: 330)CLTA4-4-9 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT ACC CAC TAGGTA GCC ATA ATC CA (SEQ ID NO: 331) CLTA4-4-10 fwd ACA CTC TTT CCC TACACG ACG CTC TTC CGA TCT CGG TCA TGT CGC TTG GAA GA (SEQ ID NO: 332)CLTA4-4-11 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTG GCC CATATT GCT TTA TGC TG (SEQ ID NO: 333) CLTA4-4-12 fwd ACA CTC TTT CCC TACACG ACG CTC TTC CGA TCT ATT AGG GGT TGG CTG CAT GA (SEQ ID NO: 334)CLTA4-4-13 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCA AGA CGTGTT GCA TGC TG (SEQ ID NO: 335) CLTA4-4-14 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TGG GAG GTG ATA AAT TCC CTA AAT (SEQ ID NO: 336)CLTA4-5-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CCA GAG ACAAAG GTG GGG AG (SEQ ID NO: 337) CLTA4-5-2 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TCA TAC AGA AGA GCA AAG TAC CA (SEQ ID NO: 338)CLTA4-5-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CAA AGA GGGGTA TCG GGA GC (SEQ ID NO: 339) CLTA4-5-4 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT AAA TGG AAG AAC CAA GTA GAT GAA (SEQ ID NO: 340)CLTA4-5-5 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT TTT TGG TTGACA GAT GGC CAC A (SEQ ID NO: 341) CLTA4-5-6 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT TCT TAC TTG TGT GAT TTT AGA ACA A (SEQ ID NO: 342)CLTA4-6-1 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GAT GGT TCATGC AGA GGG CT (SEQ ID NO: 343) CLTA4-6-2 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT GCT GGT CTT TCC TGA GCT GT (SEQ ID NO: 344)CLTA4-6-3 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT CTC CAT CAGATA CCT GTA CCC A (SEQ ID NO: 345) CLTA4-7-1 fwd ACA CTC TTT CCC TAC ACGACG CTC TTC CGA TCT GGG AAA ACA CTC TCT CTC TGC T (SEQ ID NO: 346)CLTA4-7-2 fwd ACA CTC TTT CCC TAC ACG ACG CTC TTC CGA TCT GGA GGC CACGAC ACA CAA TA (SEQ ID NO: 347) CLTA1-0-1 (Chr. 9) rev GTG ACT GGA GTTCAG ACG TGT GCT CTT CCG ATCT CAC AGG GTG GCT CTT CAG TG (SEQ ID NO: 348)CLTA1-0-1 (Chr. 12) rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGCACA TGT TTC CAC AGG GT (SEQ ID NO: 349) CLTA1-1-1 rev GTG ACT GGA GTTCAG ACG TGT GCT CTT CCG ATCT AGT GTT TCC AGG AGC GGT TT (SEQ ID NO: 350)CLTA1-2-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AAG CCT CAGGCA CAA CTC TG (SEQ ID NO: 351) CLTA1-2-2 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TAG GGG AGG GGC AAA GAC A (SEQ ID NO: 352)CLTA1-3-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGG AAC AGTGGT ATG CTG GT (SEQ ID NO: 353) CLTA1-3-2 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT AGT GTG GAC ACT GAC AAG GAA (SEQ ID NO: 354)CLTA1-4-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TCA CTG CCTGGG TGC TTT AG (SEQ ID NO: 355) CLTA1-4-2 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TAC CCC AGC CTC CAG CTT TA (SEQ ID NO: 356)CLTA1-4-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGA CTA CTGGGG AGC GAT GA (SEQ ID NO: 357) CLTA1-4-4 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT AGG CTG TTA TGC AGG AAA GGA A (SEQ ID NO: 358)CLTA1-4-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GCG GTT GAGGTG GAT GGA AG (SEQ ID NO: 359) CLTA1-4-6 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT GGC AGC ATC CCT TAC ATC CT (SEQ ID NO: 360)CLTA1-4-7 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGA AAA AGCTTC CCC AGA AAG GA (SEQ ID NO: 361) CLTA1-4-8 rev GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATCT CTG CAC CAA CCT CTA CGT CC (SEQ ID NO: 362)CLTA1-5-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CTG GAG AGGGCA TAG TTG GC (SEQ ID NO: 363) CLTA1-5-2 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TGG AAG GCT CTT TGT GGG TT (SEQ ID NO: 364)CLTA1-5-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTC CTA GCGGGA ACT GGA AA (SEQ ID NO: 365) CLTA1-5-4 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT AGG CTA ATG GGG TAG GGG AT (SEQ ID NO: 366)CLTA1-5-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGT CCA TGTTGG CTG AGG TG (SEQ ID NO: 367) CLTA1-6-1 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT CAG GCC AAC CTT GAC AAC TT (SEQ ID NO: 368)CLTA4-0-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AGC AGG CCAAAG ATG TCT CC (SEQ ID NO: 369) CLTA4-3-1 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TCT GCT CTT GAG GTT ATT TGT CC (SEQ ID NO: 370)CLTA4-3-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGG ACC AATTTG CTA CTC ATG G (SEQ ID NO: 371) CLTA4-3-3 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TGG AGG CTG TAA ACG TCC TG (SEQ ID NO: 372)CLTA4-3-4 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TGC TAT GATTTG CTG AAT TAC TCC T (SEQ ID NO: 373) CLTA4-3-5 rev GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATCT GCA ATT TTG CAG ACC ACC ATC (SEQ ID NO: 374)CLTA4-3-6 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGC AGC TTGCAA CCT TCT TG (SEQ ID NO: 375) CLTA4-3-7 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TCA TGA GAG TTT CCC CAA CA (SEQ ID NO: 376)CLTA4-4-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT ACT TGA GGGGGA AAA AGT TTC TTA (SEQ ID NO: 377) CLTA4-4-2 rev GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATCT TGG TCC CTG TCT GTC ATT GG (SEQ ID NO: 378)CLTA4-4-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT AAG CGA GTGACT GTC TGG GA (SEQ ID NO: 379) CLTA4-4-4 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT CAT GGG TGG GAC ACG TAG TT (SEQ ID NO: 380)CLTA4-4-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGC TTT CCTGGA CAC CCT ATC (SEQ ID NO: 381) CLTA4-4-6 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT AGA GCG AGG GAG CGA TGT A (SEQ ID NO: 382)CLTA4-4-7 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TTG TGG ACCACT GCT TAG TGC (SEQ ID NO: 383) CLTA4-4-8 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT CAA CTA CCC TGA GGC CAC C (SEQ ID NO: 384)CLTA4-4-9 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGT CAG CACTCC TCA GCT TT (SEQ ID NO: 385) CLTA4-4-10 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TGG AGG ATG CAT GCC ACA TT (SEQ ID NO: 386)CLTA4-4-11 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCC AGC CTCTTT GAC CCT TC (SEQ ID NO: 387) CLTA4-4-12 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT CCC ACA CCA GGC TGT AAG G (SEQ ID NO: 388)CLTA4-4-13 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT TAG ATA TATGGG TGT GTC TGT ACG (SEQ ID NO: 389) CLTA4-4-14 rev GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATCT TTC CAA AGT GGC TGA ACC AT (SEQ ID NO: 390)CLTA4-5-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCC ACA GGGCTG ATG TTT CA (SEQ ID NO: 391) CLTA4-5-2 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TTG TAA TGC AAC CTC TGT CAT GC (SEQ ID NO: 392)CLTA4-5-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CCA GCT CCAGCA ATC CAT GA (SEQ ID NO: 393) CLTA4-5-4 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT TTT GGG AAA GAT AGC CCT GGA (SEQ ID NO: 394)CLTA4-5-5 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAA TGA AACAGC GGG GAG GT (SEQ ID NO: 395) CLTA4-5-6 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT ACA ATC ACG TGT CCT TCA CT (SEQ ID NO: 396)CLTA4-6-1 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT CAG ATC CCTCCT GGG CAA TG (SEQ ID NO: 397) CLTA4-6-2 rev GTG ACT GGA GTT CAG ACGTGT GCT CTT CCG ATCT GTC AGG AGG CAA GGA GGA AC (SEQ ID NO: 398)CLTA4-6-3 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT ACT TCC TTCCTT TTG AGA CCA AGT (SEQ ID NO: 399) CLTA4-7-1 rev GTG ACT GGA GTT CAGACG TGT GCT CTT CCG ATCT GCG GCA GAT TCC TGG TGA TT (SEQ ID NO: 400)CLTA4-7-2 rev GTG ACT GGA GTT CAG ACG TGT GCT CTT CCG ATCT GGT CAC CATCAG CAC AGT CA (SEQ ID NO: 401) PE1-barcode1 CAA GCA GAA GAC GGC ATA CGAGAT ATA TCA GTG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 402)PE1-barcode2 CAA GCA GAA GAC GGC ATA CGA GAT TTT CAC CGG TGA CTG GAG TTCAGA CGT GTG CT (SEQ ID NO: 403) PE1-barcode3 CAA GCA GAA GAC GGC ATA CGAGAT CCA CTC ATG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 404)PE1-barcode4 CAA GCA GAA GAC GGC ATA CGA GAT TAC GTA CGG TGA CTG GAG TTCAGA CGT GTG CT (SEQ ID NO: 405) PE1-barcode5 CAA GCA GAA GAC GGC ATA CGAGAT CGA AAC TCG TGA CTG GAG TTC AGA CGT GTG CT (SEQ ID NO: 406)PE1-barcode6 CAA GCA GAA GAC GGC ATA CGA GAT ATC AGT ATG TGA CTG GAG TTCAGA CGT GTG CT (SEQ ID NO: 407) PE2-barcode1 AAT GAT ACG GCG ACC ACC GAGATC TAC ACA TTA CTC GAC ACT CTT TCC CTA CAC GAC (SEQ ID NO: 408)PE2-barcode2 AAT GAT ACG GCG ACC ACC GAG ATC TAC ACT CCG GAG AAC ACT CTTTCC CTA CAC GAC (SEQ ID NO: 409) PE2-barcode3 AAT GAT ACG GCG ACC ACCGAG ATC TAC ACC GCT CAT TAC ACT CTT TCC CTA CAC GAC (SEQ ID NO: 410)

REFERENCES

-   1. Hockemeyer, D. et al. Genetic engineering of human pluripotent    cells using TALE nucleases. Nature biotechnology 29, 731-734 (2011).-   2. Zou, J. et al. Gene targeting of a disease-related gene in human    induced pluripotent stem and embryonic stem cells. Cell stem cell 5,    97-110 (2009).-   3. Hockemeyer, D. et al. Efficient targeting of expressed and silent    genes in human ESCs and iPSCs using zinc-finger nucleases. Nature    biotechnology 27, 851-857 (2009).-   4. Doyon, Y. et al. Heritable targeted gene disruption in zebrafish    using designed zinc-finger nucleases. Nature biotechnology 26,    702-708 (2008).-   5. Meng, X., Noyes, M. B., Zhu, L. J., Lawson, N. D. & Wolfe, S. A.    Targeted gene inactivation in zebrafish using engineered zinc-finger    nucleases. Nature biotechnology 26, 695-701 (2008).-   6. Sander, J. D. et al. Targeted gene disruption in somatic    zebrafish cells using engineered TALENs. Nature biotechnology 29,    697-698 (2011).-   7. Tesson, L. et al. Knockout rats generated by embryo    microinjection of TALENs. Nature biotechnology 29, 695-696 (2011).-   8. Cui, X. et al. Targeted integration in rat and mouse embryos with    zinc-finger nucleases.

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-   9. Perez, E. E. et al. Establishment of HIV-1 resistance in CD4+ T    cells by genome editing using zinc-finger nucleases. Nature    biotechnology 26, 808-816 (2008).-   10. NCT00842634, NCT01044654, NCT01252641, NCT01082926.-   11. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease    in adaptive bacterial immunity. Science 337, 816-821 (2012).-   12. Cong, L. et al. Multiplex genome engineering using CRISPR/Cas    systems. Science 339, 819-823 (2013).-   13. Mali, P. et al. RNA-guided human genome engineering via Cas9.    Science 339, 823-826 (2013).-   14. Hwang, W. Y. et al. Efficient genome editing in zebrafish using    a CRISPR-Cas system.

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-   15. Jinek, M. et al. RNA-programmed genome editing in human cells.    eLife 2, e00471 (2013).-   16. Dicarlo, J. E. et al. Genome engineering in Saccharomyces    cerevisiae using CRISPR-Cas systems. Nucleic acids research (2013).-   17. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A.    RNA-guided editing of bacterial genomes using CRISPR-Cas systems.    Nature biotechnology 31, 233-239 (2013).-   18. Sapranauskas, R. et al. The Streptococcus thermophilus    CRISPR/Cas system provides immunity in Escherichia coli. Nucleic    acids research 39, 9275-9282 (2011).-   19. Semenova, E. et al. Interference by clustered regularly    interspaced short palindromic repeat (CRISPR) RNA is governed by a    seed sequence. Proceedings of the National Academy of Sciences of    the United States of America 108, 10098-10103 (2011).-   20. Qi, L. S. et al. Repurposing CRISPR as an RNA-Guided Platform    for Sequence-Specific

Control of Gene Expression. Cell 152, 1173-1183 (2013).

-   21. Pattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R.    Revealing off-target cleavage specificities of zinc-finger nucleases    by in vitro selection. Nature methods 8, 765-770 (2011).-   22. Doyon, J. B., Pattanayak, V., Meyer, C. B. & Liu, D. R. Directed    evolution and substrate specificity profile of homing endonuclease    I-SceI. Journal of the American Chemical Society 128, 2477-2484    (2006).-   23. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A.    RNA-guided editing of bacterial genomes using CRISPR-Cas systems.    Nature biotechnology 31, 233-239 (2013).-   24. Pattanayak, V., Ramirez, C. L., Joung, J. K. & Liu, D. R.    Revealing off-target cleavage specificities of zinc-finger nucleases    by in vitro selection. Nature methods 8, 765-770 (2011).-   25. Schneider, T. D. & Stephens, R. M. Sequence logos: a new way to    display consensus sequences. Nucleic acids research 18, 6097-6100    (1990).

All publications, patents and sequence database entries mentionedherein, including those items listed above, are hereby incorporated byreference in their entirety as if each individual publication or patentwas specifically and individually indicated to be incorporated byreference. In case of conflict, the present application, including anydefinitions herein, will control.

What is claimed is:
 1. A method for identifying a target site of aRNA-programmable nuclease, the method comprising (a) providing anuclease that cuts a double-stranded nucleic acid target site, whereincutting of the target site results in cut nucleic acid strandscomprising a 5′ phosphate moiety; (b) contacting the nuclease of (a)with a library of candidate nucleic acid molecules, wherein each nucleicacid molecule comprises a concatemer of a sequence comprising acandidate nuclease target site and a constant insert sequence, underconditions suitable for the nuclease to cut a candidate nucleic acidmolecule comprising a target site of the nuclease; and (c) identifyingnuclease target sites cut by the nuclease in (b) by determining thesequence of an uncut nuclease target site on the nucleic acid strandthat was cut by the nuclease in step (b).
 2. The method of claim 1,wherein the method identifies off-target sites of the RNA-programmablenuclease.
 3. The method of claim 1, wherein the nuclease creates bluntends.
 4. The method of claim 1, wherein the nuclease creates a 5′overhang.
 5. The method of claim 1, wherein the determining of step (c)comprises ligating a first nucleic acid adapter to the 5′ end of anucleic acid strand that was cut by the nuclease in step (b) via5′-phosphate-dependent ligation.
 6. The method of claim 5, wherein thenucleic acid adapter is provided in double-stranded form.
 7. The methodof claim 6, wherein the 5′-phosphate-dependent ligation is a blunt endligation.
 8. The method of claim 5, wherein the method comprises fillingin the 5′-overhang before ligating the first nucleic acid adapter to thenucleic acid strand that was cut by the nuclease.
 9. The method of claim5, wherein the determining of step (c) further comprises amplifying afragment of the concatemer cut by the nuclease that comprises an uncuttarget site via a PCR reaction using a PCR primer that hybridizes withthe adapter and a PCR primer that hybridizes with the constant insertsequence.
 10. The method of claim 9, wherein the method furthercomprises enriching the amplified nucleic acid molecules for moleculescomprising a single uncut target sequence.
 11. The method of claim 1,wherein the determining of step (c) comprises sequencing the nucleicacid strand that was cut by the nuclease in step (b), or a copy thereofobtained via PCR.
 12. The method of claim 1, wherein the library ofcandidate nucleic acid molecules comprises at least 10⁸, at least 10⁹,at least 10¹⁰, at least 10¹¹, or at least 10¹² different candidatenuclease cleavage sites.
 13. The method of claim 1, wherein the nucleaseis a therapeutic nuclease which cuts a specific nuclease target site ina gene associated with a disease.
 14. The method of claim 13 furthercomprising determining a maximum concentration of the therapeuticnuclease at which the therapeutic nuclease cuts the specific nucleasetarget site, and does not cut more than 10, more than 5, more than 4,more than 3, more than 2, more than 1, or no additional nuclease targetsites.
 15. The method of claim 14, further comprising administering thetherapeutic nuclease to a subject in an amount effective to generate afinal concentration equal or lower than the maximum concentration. 16.The method of claim 1, wherein the nuclease is an RNA-programmablenuclease that forms a complex with an RNA molecule, and wherein thenuclease:RNA complex specifically binds a nucleic acid sequencecomplementary to the sequence of the RNA molecule.
 17. The method ofclaim 16, wherein the RNA molecule is a single-guide RNA (sgRNA). 18.The method of claim 16, wherein the sgRNA comprises 15-25, 19-21, or 20nucleotides that are complementary to the target sequence.
 19. Themethod of claim 1, wherein the nuclease is a Cas9 nuclease.
 20. Themethod of claim 16, wherein the nuclease target site comprises a[sgRNA-complementary sequence]-[protospacer adjacent motif (PAM)]structure, and the nuclease cuts the target site within thesgRNA-complementary sequence.
 21. The method of claim 20, wherein thesgRNA-complementary sequence comprises 10, 11, 12, 13, 14, 15, 16, 17,18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides. 22.The method of claim 1, wherein the nuclease comprises an unspecificnucleic acid cleavage domain.
 23. The method of claim 22, wherein thenuclease comprises a FokI cleavage domain.
 24. The method of claim 22,wherein the nuclease comprises a nucleic acid cleavage domain thatcleaves a target sequence upon cleavage domain dimerization.